\ Downloads for data in this track are available:\
\ This track shows multiple alignments of 26 nematode\ species and measurements of evolutionary conservation using\ two methods (phastCons and phyloP) from the\ \ PHAST package, for all 26 species.\ The multiple alignments were generated using multiz and \ other tools in the UCSC/Penn State Bioinformatics\ comparative genomics alignment pipeline.\ Conserved elements identified by phastCons are also displayed in\ this track.\
\\ PhastCons is a hidden Markov model-based method that estimates the probability that each\ nucleotide belongs to a conserved element, based on the multiple alignment.\ It considers not just each individual alignment column, but also its\ flanking columns. By contrast, phyloP separately measures conservation at\ individual columns, ignoring the effects of their neighbors. As a\ consequence, the phyloP plots have a less smooth appearance than the\ phastCons plots, with more "texture" at individual sites. The two methods\ have different strengths and weaknesses. PhastCons is sensitive to "runs"\ of conserved sites, and is therefore effective for picking out conserved\ elements. PhyloP, on the other hand, is more appropriate for evaluating\ signatures of selection at particular nucleotides or classes of nucleotides\ (e.g., third codon positions, or first positions of miRNA target sites).\
\\ Another important difference is that phyloP can measure acceleration\ (faster evolution than expected under neutral drift) as well as\ conservation (slower than expected evolution). In the phyloP plots, sites\ predicted to be conserved are assigned positive scores (and shown in blue),\ while sites predicted to be fast-evolving are assigned negative scores (and\ shown in red). The absolute values of the scores represent -log p-values\ under a null hypothesis of neutral evolution. The phastCons scores, by\ contrast, represent probabilities of negative selection and range between 0\ and 1.\
\\ Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as\ missing data, and both were run with the same parameters.\
\ \\ UCSC has repeatmasked and aligned all genome assemblies, and\ provides all the sequences for download. For genome assemblies\ not available in the genome browser, there are alternative browser\ views in the preview genome browser. \ The species aligned for this track include 26 nematode genome sequences.\ Compared to the previous 6-nematode alignment (ce11),\ this track includes 4 new nematode genomes and 2 nematode genomes with updated\ sequence assemblies (Table 1). The four new species are the\ assemblies: H. contortus (haeCon1) at an unknown coverage,\ M. Hapla (melHap1) at 10.4X coverage, M. incognita (melInc1) at 5X coverage,\ and B. Malayi (bruMal1) at 9X coverage.\ The C. Japonica (22X, caeJap3) and P. pacificus (8.92X, priPac2) assemblies\ have been updated from those used in the previous 6-species nematode alignment.\
\\
\ \\
\ Organism Species Release date UCSC/WormBase
versionalignment type \ C. elegans Caenorhabditis elegans \ Aug. 2014 ce11/WBcel235/GCA_000002985.3 reference species \ C. brenneri Caenorhabditis brenneri \ Nov. 2010 caePb3/WS227_C. brenneri 6.0.1b MAF Net \ C. remanei Caenorhabditis remanei \ Jul. 2007 caeRem4/WS220 MAF Net \ C. briggsae Caenorhabditis briggsae \ Apr. 2011 cb4/WS225 MAF Net \ C. japonica Caenorhabditis japonica \ Aug. 2010 caeJap4/WS227_WUSTL 7.0.1/GCA_000147155.1 MAF Net \ C. tropicalis Caenorhabditis tropicalis \ Nov. 2010 caeSp111/WS226_WUSTL 3.0.1 MAF Net \ C. angaria Caenorhabditis angaria \ Apr. 2012 caeAng2/WS232/ps1010rel8 MAF Net \ C. sp. 5 ju800 Caenorhabditis sp5 ju800 \ Jan. 2012 caeSp51/WS230_Caenorhabditis_sp_5-JU800-1.0 MAF Net \ H. bacteriophora/m31e Heterorhabditis bacteriophora \ Aug. 2011 hetBac1/WS229_H. bacteriophora 7.0/GCA_000223415.1 MAF Net \ Threadworm Strongyloides ratti \ Sep. 2014 strRat2/S. ratti ED321/GCA_001040885.1 MAF Net \ Microworm Panagrellus redivivus \ Feb. 2013 panRed1/WS240_Pred3/GCA_000341325.1 MAF Net \ A. ceylanicum Ancylostoma ceylanicum \ Mar. 2014 ancCey1/WS243_Acey_2013.11.30.genDNA/GCA_000688135.1 MAF Net \ N. americanus Necator americanus \ Dec. 2013 necAme1/WS242_N_americanus_v1/GCA_000507365.1 MAF Net \ Barber pole worm Haemonchus contortus \ Jul. 2013 haeCon2/WS239_Haemonchus_contortus_MHco3-2.0 MAF Net \ Pig roundworm Ascaris suum \ Sep. 2012 ascSuu1/GCA_000298755.1 MAF Net \ P. exspectatus Pristionchus exspectatus \ Mar. 2014 priExs1/WS243_P_exspectatus_v1 MAF Net \ P. pacificus Pristionchus pacificus \ Aug. 2014 priPac3/WS221_P_pacificus-v2 MAF Net \ M. hapla Meloidogyne hapla \ Sep. 2008 melHap1/WS210_M. hapla VW9 MAF Net \ M. incognita Meloidogyne incognita \ Feb. 2008 melInc2/WS245_M. incognita PRJEA28837 MAF Net \ Pine wood nematode Bursaphelenchus xylophilus \ Nov. 2011 burXyl1/WS229_B. xylophilus Ka4C1 MAF Net \ Dog heartworm Dirofilaria immitis \ Sep. 2013 dirImm1/WS240_D. immitis v2.2 MAF Net \ Eye worm Loa loa \ Jul. 2012 loaLoa1/WS235_L_loa_Cameroon_isolate/GCA_000183805.3 MAF Net \ O. volvulus Onchocerca volvulus \ Nov. 2013 oncVol1/WS241_O_volvulus_Cameroon_v3/GCA_000499405.1 MAF Net \ Filarial worm Brugia malayi \ May. 2014 bruMal2/WS244_B_malayi-3.1 MAF Net \ Trichinella Trichinella spiralis \ Jan. 2011 triSpi1/WS225_Trichinella_spiralis-3.7.1/GCA_000181795.2 MAF Net \ Whipworm Trichuris suis \ Jul. 2014 triSui1/WS243_T. suis DCEP-RM93M male/GCA_000701005.1 MAF Net
\ Table 1. Genome assemblies included in the 26-way Conservation \ track.\
\ In full and pack display modes, conservation scores are displayed as a\ wiggle track (histogram) in which the height reflects the \ size of the score. \ The conservation wiggles can be configured in a variety of ways to \ highlight different aspects of the displayed information. \ Click the Graph configuration help link for an explanation \ of the configuration options.
\\ Pairwise alignments of each species to the C. elegans genome are \ displayed below the conservation histogram as a grayscale density plot (in \ pack mode) or as a wiggle (in full mode) that indicates alignment quality.\ In dense display mode, conservation is shown in grayscale using\ darker values to indicate higher levels of overall conservation \ as scored by phastCons.
\\ Checkboxes on the track configuration page allow selection of the\ species to include in the pairwise display. \ Note that excluding species from the pairwise display does not alter the\ the conservation score display.
\\ To view detailed information about the alignments at a specific\ position, zoom the display in to 30,000 or fewer bases, then click on\ the alignment.
\ \\ The Display chains between alignments configuration option \ enables display of gaps between alignment blocks in the pairwise alignments in \ a manner similar to the Chain track display. The following\ conventions are used:\
\ Discontinuities in the genomic context (chromosome, scaffold or region) of the\ aligned DNA in the aligning species are shown as follows: \
\ When zoomed-in to the base-level display, the track shows the base \ composition of each alignment. \ The numbers and symbols on the Gaps\ line indicate the lengths of gaps in the C. elegans sequence at those \ alignment positions relative to the longest non-C. elegans sequence. \ If there is sufficient space in the display, the size of the gap is shown. \ If the space is insufficient and the gap size is a multiple of 3, a \ "*" is displayed; other gap sizes are indicated by "+".
\\ Codon translation is available in base-level display mode if the\ displayed region is identified as a coding segment. To display this annotation,\ select the species for translation from the pull-down menu in the Codon\ Translation configuration section at the top of the page. Then, select one of\ the following modes:\
\ Codon translation uses the following gene tracks as the basis for\ translation, depending on the species chosen (Table 2). \ Species listed in the row labeled "None" do not have \ species-specific reading frames for gene translation.\ \
\ \\
\ Table 2. Gene tracks used for codon translation.\\ Gene Track Species \ WS245 Worm Base Genes \ A. ceylanicum, Barber pole worm/H. contortus, C. angaria, C. brenneri, C. briggsae, C. elegans,\ C. japonica, C. remanei, C. sp. 5 ju800, C. tropicalis, Dog heartworm/D. immitis, Eye worm/L. loa,\ Filarial worm/B. malayi, H. bacteriophora/m31e, Microworm/P. redivivus, M. hapla, M. incognita,\ N. americanus, O. volvulus, P. exspectatus, P. pacificus, Pine wood nematode/B. xylophilus,\ Trichinella/T. spiralis, Whipworm/T. suis \ NCBI gene annotations Threadworm/S. ratti \ no annotation Pig roundworm/A. suum
\ Pairwise alignments with the C. elegans genome were generated for \ each species using lastz from repeat-masked genomic sequence. \ Pairwise alignments were then linked into chains using a dynamic programming\ algorithm that finds maximally scoring chains of gapless subsections\ of the alignments organized in a kd-tree.\ All pairwise alignment and chaining parameters are the same for all pairs.\ See also: nematode 26-way alignment parameters.\ High-scoring chains were then placed along the genome, with\ gaps filled by lower-scoring chains, to produce an alignment net.\ For more information about the chaining and netting process and \ parameters for each species, see the description pages for the Chain and Net \ tracks.
\\ The resulting best-in-genome pairwise alignments\ were progressively aligned using multiz/autoMZ, \ following the tree topology diagrammed above, to produce multiple alignments.\ The multiple alignments were post-processed to\ add annotations indicating alignment gaps, genomic breaks,\ and base quality of the component sequences.\ The annotated multiple alignments, in MAF format, are available for\ bulk download.\ An alignment summary table containing an entry for each\ alignment block in each species was generated to improve\ track display performance at large scales.\ Framing tables were constructed to enable\ visualization of codons in the multiple alignment display.
\ \\ Both phastCons and phyloP are phylogenetic methods that\ rely on a tree model containing the tree topology,\ branch lengths representing evolutionary distance at neutrally\ evolving sites, the background distribution of nucleotides, and a substitution\ rate matrix. The \ nematode tree model for this track was\ generated using the phyloFit program from the PHAST package \ (REV model, EM algorithm, medium precision) using multiple alignments of \ 4-fold degenerate sites extracted from the 26-way alignment\ (msa_view). The 4d sites were derived from the WormBase/Sanger gene set\ of C. elegans, filtered to select single-coverage long transcripts.\
\\ The phastCons program computes conservation scores based on a phylo-HMM, a\ type of probabilistic model that describes both the process of DNA\ substitution at each site in a genome and the way this process changes from\ one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and\ Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for\ conserved regions and a state for non-conserved regions. The value plotted\ at each site is the posterior probability that the corresponding alignment\ column was "generated" by the conserved state of the phylo-HMM. These\ scores reflect the phylogeny (including branch lengths) of the species in\ question, a continuous-time Markov model of the nucleotide substitution\ process, and a tendency for conservation levels to be autocorrelated along\ the genome (i.e., to be similar at adjacent sites). The general reversible\ (REV) substitution model was used. Unlike many conservation-scoring programs, \ phastCons does not rely on a sliding window\ of fixed size; therefore, short highly-conserved regions and long moderately\ conserved regions can both obtain high scores. \ More information about\ phastCons can be found in Siepel et al. 2005.
\\ The phastCons parameters were tuned to produce approximately 70% conserved\ elements in the C. elegans WormBase/Sanger gene coding regions.\ This parameter set (expected-length=15, target-coverage=0.3, rho=0.3) was\ then used to generate the nematode and caenorhabditis conservation scoring.
\ \\ The phyloP program supports several different methods for computing\ p-values of conservation or acceleration, for individual nucleotides or\ larger elements\ (http://compgen.cshl.edu/phast/).\ Here it was used\ to produce separate scores at each base (--wig-scores option), considering\ all branches of the phylogeny rather than a particular subtree or lineage\ (i.e., the --subtree option was not used). The scores were computed by\ performing a likelihood ratio test at each alignment column (--method LRT),\ and scores for both conservation and acceleration were produced (--mode\ CONACC). \
\\ The conserved elements were predicted by running phastCons with the\ --most-conserved (aka --viterbi) option. The predicted elements are\ segments of the alignment\ that are likely to have been "generated" by the conserved state of the\ phylo-HMM. Each element is assigned a log-odds score equal to its log\ probability under the conserved model minus its log probability under the\ non-conserved model. The "score" field associated with this track contains\ transformed log-odds scores, taking values between 0 and 1000. (The scores\ are transformed using a monotonic function of the form a * log(x) + b.) The\ raw log odds scores are retained in the "name" field and can be seen on the\ details page or in the browser when the track's display mode is set to\ "pack" or "full".\
\ \This track was created using the following programs:\
The phylogenetic tree is based on Kiontke et al. (2007).\
\ \\ Felsenstein J, Churchill GA.\ A Hidden Markov Model approach to\ variation among sites in rate of evolution.\ Mol Biol Evol. 1996 Jan;13(1):93-104.\ PMID: 8583911\
\ \\
Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A.\
\
Detection of nonneutral substitution rates on mammalian phylogenies.\
Genome Res. 2010 Jan;20(1):110-21.\
PMID: 19858363; PMC:
\
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K,\
Clawson H, Spieth J, Hillier LW, Richards S, et al.\
Evolutionarily conserved elements in vertebrate, insect, worm,\
and yeast genomes.\
Genome Res. 2005 Aug;15(8):1034-50.\
PMID: 16024819; PMC:
\ Siepel A, Haussler D.\ Phylogenetic Hidden Markov Models.\ In: Nielsen R, editor. Statistical Methods in Molecular Evolution.\ New York: Springer; 2005. pp. 325-351.\
\ \\
Yang Z.\
A space-time process model for the evolution of DNA\
sequences.\
Genetics. 1995 Feb;139(2):993-1005.\
PMID: 7713447; PMC:
\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes.\
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.\
PMID: 14500911; PMC:
\
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM,\
Baertsch R, Rosenbloom K, Clawson H, Green ED, et al.\
Aligning multiple genomic sequences with the threaded blockset aligner.\
Genome Res. 2004 Apr;14(4):708-15.\
PMID: 15060014; PMC:
\ Harris RS.\ Improved pairwise alignment of genomic DNA.\ Ph.D. Thesis. Pennsylvania State University, USA. 2007.\
\ \\ Chiaromonte F, Yap VB, Miller W.\ Scoring pairwise genomic sequence alignments.\ Pac Symp Biocomput. 2002:115-26.\ PMID: 11928468\
\ \\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
Human-mouse alignments with BLASTZ.\
Genome Res. 2003 Jan;13(1):103-7.\
PMID: 12529312; PMC:
\ Kiontke K, Barrière A, Kolotuev I, Podbilewicz B, Sommer R, Fitch DH, Félix MA.\ \ Trends, stasis, and drift in the evolution of nematode vulva development.\ Curr Biol. 2007 Nov 20;17(22):1925-37.\ PMID: 18024125\
\ compGeno 1 compositeTrack on\ dragAndDrop subTracks\ group compGeno\ longLabel Nematode Multiz Alignment & Conservation (26 Species)\ priority 1\ shortLabel Conservation\ subGroup1 view Views align=Multiz_Alignments phyloP=Basewise_Conservation_(phyloP) phastcons=Element_Conservation_(phastCons) elements=Conserved_Elements\ track cons26way\ type bed 4\ visibility hide\ cons26wayViewelements Conserved Elements bed 4 Nematode Multiz Alignment & Conservation (26 Species) 1 1 0 0 0 127 127 127 0 0 0 compGeno 1 longLabel Nematode Multiz Alignment & Conservation (26 Species)\ parent cons26way\ shortLabel Conserved Elements\ track cons26wayViewelements\ view elements\ visibility dense\ cpgIslandExt CpG Islands bed 4 + CpG Islands (Islands < 300 Bases are Light Green) 3 1 0 100 0 128 228 128 0 0 0CpG islands are associated with genes, particularly housekeeping\ genes, in vertebrates. CpG islands are typically common near\ transcription start sites and may be associated with promoter\ regions. Normally a C (cytosine) base followed immediately by a \ G (guanine) base (a CpG) is rare in\ vertebrate DNA because the Cs in such an arrangement tend to be\ methylated. This methylation helps distinguish the newly synthesized\ DNA strand from the parent strand, which aids in the final stages of\ DNA proofreading after duplication. However, over evolutionary time,\ methylated Cs tend to turn into Ts because of spontaneous\ deamination. The result is that CpGs are relatively rare unless\ there is selective pressure to keep them or a region is not methylated\ for some other reason, perhaps having to do with the regulation of gene\ expression. CpG islands are regions where CpGs are present at\ significantly higher levels than is typical for the genome as a whole.
\ \\ The unmasked version of the track displays potential CpG islands\ that exist in repeat regions and would otherwise not be visible\ in the repeat masked version.\
\ \\ By default, only the masked version of the track is displayed. To view the\ unmasked version, change the visibility settings in the track controls at\ the top of this page.\
\ \CpG islands were predicted by searching the sequence one base at a\ time, scoring each dinucleotide (+17 for CG and -1 for others) and\ identifying maximally scoring segments. Each segment was then\ evaluated for the following criteria:\ \
\ The entire genome sequence, masking areas included, was\ used for the construction of the track Unmasked CpG.\ The track CpG Islands is constructed on the sequence after\ all masked sequence is removed.\
\ \The CpG count is the number of CG dinucleotides in the island. \ The Percentage CpG is the ratio of CpG nucleotide bases\ (twice the CpG count) to the length. The ratio of observed to expected \ CpG is calculated according to the formula (cited in \ Gardiner-Garden et al. (1987)):\ \
Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)\ \ where N = length of sequence.\
\ The calculation of the track data is performed by the following command sequence:\
\
twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \\\
| cpg_lh /dev/stdin 2> cpg_lh.err \\\
| awk '{$2 = $2 - 1; width = $3 - $2; printf("%s\\t%d\\t%s\\t%s %s\\t%s\\t%s\\t%0.0f\\t%0.1f\\t%s\\t%s\\n", $1, $2, $3, $5, $6, width, $6, width*$7*0.01, 100.0*2*$6/width, $7, $9);}' \\\
| sort -k1,1 -k2,2n > cpgIsland.bed\
\
The unmasked track data is constructed from\
twoBitToFa -noMask output for the twoBitToFa command.\
\
\
\ CpG islands and its associated tables can be explored interactively using the\ REST API, the\ Table Browser or the\ Data Integrator.\ All the tables can also be queried directly from our public MySQL\ servers, with more information available on our\ help page as well as on\ our blog.
\\ The source for the cpg_lh program can be obtained from\ src/utils/cpgIslandExt/.\ The cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose "save file")\
\ \This track was generated using a modification of a program developed by G. Miklem and L. Hillier \ (unpublished).
\ \\ Gardiner-Garden M, Frommer M.\ \ CpG islands in vertebrate genomes.\ J Mol Biol. 1987 Jul 20;196(2):261-82.\ PMID: 3656447\
\ regulation 1 html cpgIslandSuper\ longLabel CpG Islands (Islands < 300 Bases are Light Green)\ parent cpgIslandSuper pack\ priority 1\ shortLabel CpG Islands\ track cpgIslandExt\ cons26wayViewphastcons Element Conservation (phastCons) bed 4 Nematode Multiz Alignment & Conservation (26 Species) 2 1 0 0 0 127 127 127 0 0 0 compGeno 1 longLabel Nematode Multiz Alignment & Conservation (26 Species)\ parent cons26way\ shortLabel Element Conservation (phastCons)\ track cons26wayViewphastcons\ view phastcons\ visibility full\ cons26wayViewalign Multiz Alignments bed 4 Nematode Multiz Alignment & Conservation (26 Species) 3 1 0 0 0 127 127 127 0 0 0 compGeno 1 longLabel Nematode Multiz Alignment & Conservation (26 Species)\ parent cons26way\ shortLabel Multiz Alignments\ track cons26wayViewalign\ view align\ viewUi on\ visibility pack\ ncbiRefSeq RefSeq All genePred NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, YP_*) 1 1 12 12 120 133 133 187 0 0 0 genes 1 baseColorDefault genomicCodons\ baseColorUseCds given\ color 12,12,120\ idXref ncbiRefSeqLink mrnaAcc name\ longLabel NCBI RefSeq genes, curated and predicted (NM_*, XM_*, NR_*, XR_*, NP_*, YP_*)\ parent refSeqComposite on\ priority 1\ shortLabel RefSeq All\ track ncbiRefSeq\ chainCaeRem4 caeRem4 Chain chain caeRem4 C. remanei (Jul. 2007 (WS220/caeRem4)) Chained Alignments 3 2 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel C. remanei (Jul. 2007 (WS220/caeRem4)) Chained Alignments\ otherDb caeRem4\ parent nematodesChainNetViewchain off\ shortLabel caeRem4 Chain\ subGroups view=chain species=s001 clade=c00\ track chainCaeRem4\ type chain caeRem4\ cons135wayViewphyloP Basewise Conservation (phyloP) bed 4 Multiz Alignment & Conservation (135 species: 112 nematodes, 22 flatworms and Ciona intestinalis) 2 2 0 0 0 127 127 127 0 0 0 compGeno 1 longLabel Multiz Alignment & Conservation (135 species: 112 nematodes, 22 flatworms and Ciona intestinalis)\ parent cons135way\ shortLabel Basewise Conservation (phyloP)\ track cons135wayViewphyloP\ view phyloP\ viewLimits -20.0:9.869\ viewLimitsMax -20:0.869\ visibility full\ cons135way Cons 135 species bed 4 Multiz Alignment & Conservation (135 species: 112 nematodes, 22 flatworms and Ciona intestinalis) 2 2 0 0 0 127 127 127 0 0 0\ This track shows multiple alignments of 135 species: 112 nematodes,\ 22 flatworms and one Ciona intestinalis sequence and measurements of\ evolutionary conservation using\ two methods (phastCons and phyloP) from the\ \ PHAST package, for all 135 species.\ The multiple alignments were generated using multiz and\ other tools in the UCSC/Penn State Bioinformatics\ comparative genomics alignment pipeline.\ Conserved elements identified by phastCons are also displayed in\ this track.\
\\ The phylogenetic tree was derived from kmers in common counting\ between the sequences to obtain a 'distance' matrix, then using the\ phylip command 'neighbors' operation for the simple neighbor joining\ algorithm to establish this binary tree. This tree is not necessarily\ biologically correct, but it does serve as a useful guide tree for the\ multiz alignment procedure. See also:\ Phylip distance operations, \ assembly and alignment-free phylogeny reconstruction, and \ recapitulating phylogenies using k-mers.\
\\ PhastCons (which has been used in previous Conservation tracks) is a hidden\ Markov model-based method that estimates the probability that each\ nucleotide belongs to a conserved element, based on the multiple alignment.\ It considers not just each individual alignment column, but also its\ flanking columns. By contrast, phyloP separately measures conservation at\ individual columns, ignoring the effects of their neighbors. As a\ consequence, the phyloP plots have a less smooth appearance than the\ phastCons plots, with more "texture" at individual sites. The two methods\ have different strengths and weaknesses. PhastCons is sensitive to "runs"\ of conserved sites, and is therefore effective for picking out conserved\ elements. PhyloP, on the other hand, is more appropriate for evaluating\ signatures of selection at particular nucleotides or classes of nucleotides\ (e.g., third codon positions, or first positions of miRNA target sites).\
\\ Another important difference is that phyloP can measure acceleration\ (faster evolution than expected under neutral drift) as well as\ conservation (slower than expected evolution). In the phyloP plots, sites\ predicted to be conserved are assigned positive scores (and shown in blue),\ while sites predicted to be fast-evolving are assigned negative scores (and\ shown in red). The absolute values of the scores represent -log p-values\ under a null hypothesis of neutral evolution. The phastCons scores, by\ contrast, represent probabilities of negative selection and range between 0\ and 1.\
\\ Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as\ missing data.\
\\ See also: lastz parameters and other details, and\ chain minimum score and gap parameters used in these alignments.\
\ \ \\ Missing sequence in the assemblies is highlighted in the track display\ by regions of yellow when zoomed out and Ns displayed at base\ level (see Gap Annotation, below).
\\
\ \ Downloads for data in this track are available:\\
\ Organism Species Assembly name browser or
NCBI sourcealignment type \ C. elegans Caenorhabditis elegans \Feb. 2013 (WBcel235/ce11) \Feb. 2013 (WBcel235/ce11) \reference \ A. ceylanicum Ancylostoma ceylanicum \Mar. 2014 (WS243/Acey_2013.11.30.genDNA/ancCey1) \Mar. 2014 (WS243/Acey_2013.11.30.genDNA/ancCey1) \net \ Acrobeloides_nanus Acrobeloides nanus \Jun. 2018 (v1) \GCA_900406225.1 \net \ Ancylostoma_caninum Ancylostoma caninum \Jul. 2018 (A_caninum_9.3.2.ec.cg.pg) \GCA_003336725.1 \net \ Ancylostoma_duodenale Ancylostoma duodenale \Jan. 2015 (A_duodenale_2.2.ec.cg.pg) \GCA_000816745.1 \net \ Angiostrongylus_cantonensis Angiostrongylus cantonensis \Nov. 2016 (ASM188428v1) \GCA_001884285.1 \net \ Ascaris_suum Ascaris suum \Nov. 2017 (ASM18702v3) \GCA_000187025.3 \net \ Barber pole worm Haemonchus contortus \Jul. 2013 (WormBase WS239/haeCon2) \Jul. 2013 (WormBase WS239/haeCon2) \net \ Brugia_malayi Brugia malayi \Mar. 2008 (ASM299v2) \GCF_000002995.3 \net \ Brugia_pahangi Brugia pahangi \Sep. 2015 (Brugia_pa_1.0) \GCA_001280985.1 \net \ Bursaphelenchus_xylophilus Bursaphelenchus xylophilus \Oct. 2011 (ASM23113v1) \GCA_000231135.1 \net \ C. angaria Caenorhabditis angaria \Apr. 2012 (WS232/ps1010rel8/caeAng2) \Apr. 2012 (WS232/ps1010rel8/caeAng2) \net \ C. brenneri Caenorhabditis brenneri \Nov. 2010 (C. brenneri 6.0.1b/caePb3) \Nov. 2010 (C. brenneri 6.0.1b/caePb3) \net \ C. briggsae Caenorhabditis briggsae \Apr. 2011 (WS225/cb4) \Apr. 2011 (WS225/cb4) \net \ C. intestinalis Ciona intestinalis \Apr. 2011 (Kyoto KH/ci3) \Apr. 2011 (Kyoto KH/ci3) \net \ C. japonica Caenorhabditis japonica \Aug. 2010 (WUSTL 7.0.1/caeJap4) \Aug. 2010 (WUSTL 7.0.1/caeJap4) \net \ C. remanei Caenorhabditis remanei \Jul. 2007 (WS220/caeRem4) \Jul. 2007 (WS220/caeRem4) \net \ C. sp. 5 ju800 Caenorhabditis sp5 ju800 \Jan. 2012 (WS230/Caenorhabditis_sp_5-JU800-1.0/caeSp51) \Jan. 2012 (WS230/Caenorhabditis_sp_5-JU800-1.0/caeSp51) \net \ C. tropicalis Caenorhabditis tropicalis \Nov. 2010 (WS226/WUSTL 3.0.1/caeSp111) \Nov. 2010 (WS226/WUSTL 3.0.1/caeSp111) \net \ C_briggsae Caenorhabditis briggsae \Jul. 2014 (CB4) \GCA_000004555.3 \net \ C_latens Caenorhabditis latens \Aug. 2017 (CaeLat1.0) \GCA_002259235.1 \net \ C_nigoni Caenorhabditis nigoni \Nov. 2017 (nigoni.pc_2016.07.14) \GCA_002742825.1 \net \ C_sp21_LS_2015 Caenorhabditis sp. 21 LS-2015 \Aug. 2018 (CPARV_v1) \GCA_900536235.1 \net \ C_sp26_LS_2015 Caenorhabditis sp. 26 LS-2015 \Aug. 2018 (CZANZ_v1) \GCA_900536285.1 \net \ C_sp31_LS_2015 Caenorhabditis sp. 31 LS-2015 \Aug. 2018 (CUTEL_v1) \GCA_900536295.1 \net \ C_sp32_LS_2015 Caenorhabditis sp. 32 LS-2015 \Aug. 2018 (CSULS_v1) \GCA_900536325.1 \net \ C_sp34_TK_2017 Caenorhabditis sp. 34 TK-2017 \Jun. 2017 (Sp34_v7) \GCA_003052745.1 \net \ C_sp38_MB_2015 Caenorhabditis sp. 38 MB-2015 \Aug. 2018 (CQUIO_v1) \GCA_900536415.1 \net \ C_sp39_LS_2015 Caenorhabditis sp. 39 LS-2015 \Aug. 2018 (CWAIT_v1) \GCA_900536345.1 \net \ C_sp40_LS_2015 Caenorhabditis sp. 40 LS-2015 \Aug. 2018 (CTRIB_v1) \GCA_900536305.1 \net \ Clonorchis_sinensis Clonorchis sinensis \Nov. 2011 (C_sinensis-2.0) \GCA_000236345.1 \net \ Dicrocoelium_dendriticum Dicrocoelium dendriticum \Sep. 2014 (D_dendriticum_Leon_v1_0_4) \GCA_000950715.1 \net \ Dictyocaulus_viviparus Dictyocaulus viviparus \Mar. 2015 (D_viviparus_9.2.1.ec.pg) \GCA_000816705.1 \net \ Diploscapter_coronatus Diploscapter coronatus \Jun. 2017 (ASM220778v1) \GCA_002207785.1 \net \ Diploscapter_pachys Diploscapter pachys \Sep. 2017 (DipSp1Ass11Ann3) \GCA_002287525.1 \net \ Dirofilaria_immitis Dirofilaria immitis \Aug. 2013 (ASM107739v1) \GCA_001077395.1 \net \ Ditylenchus_destructor Ditylenchus destructor \Mar. 2016 (ASM157970v1) \GCA_001579705.1 \net \ Dog heartworm Dirofilaria immitis \Sep. 2013 (WS240/D. immitis v2.2/dirImm1) \Sep. 2013 (WS240/D. immitis v2.2/dirImm1) \net \ Dugesia_japonica Dugesia japonica \Jan. 2017 (Djap_assembly_v1) \GCA_001938525.1 \net \ Echinococcus_canadensis Echinococcus canadensis \May 2016 (ECANG7) \GCA_900004735.1 \net \ Echinococcus_granulosus Echinococcus granulosus \Jan. 2014 (ASM52419v1) \GCA_000524195.1 \net \ Echinococcus_multilocularis Echinococcus multilocularis \Dec. 2015 (EMULTI002) \GCA_000469725.3 \net \ Elaeophora_elaphi Elaeophora elaphi \Nov. 2013 (EEL001) \GCA_000499685.1 \net \ Eye worm Loa loa \Jul. 2012 (WS235/L_loa_Cameroon_isolate/loaLoa1) \Jul. 2012 (WS235/L_loa_Cameroon_isolate/loaLoa1) \net \ Fasciola_gigantica Fasciola gigantica \Jan. 2018 (ASM286751v1) \GCA_002867515.1 \net \ Fasciola_hepatica Fasciola hepatica \Apr. 2018 (Fasciola_10x_pilon) \GCA_900302435.1 \net \ Filarial worm Brugia malayi \May. 2014 (WS244/B_malayi-3.1/bruMal2) \May. 2014 (WS244/B_malayi-3.1/bruMal2) \net \ Girardia_tigrina Girardia tigrina \Jan. 2017 (gtig.1) \GCA_001938485.1 \net \ Globodera_ellingtonae Globodera ellingtonae \Sep. 2016 (ASM172322v1) \GCA_001723225.1 \net \ Globodera_pallida Globodera pallida \May 2014 (GPAL001) \GCA_000724045.1 \net \ Globodera_rostochiensis Globodera rostochiensis \Apr. 2016 (nGr) \GCA_900079975.1 \net \ Gyrodactylus_salaris Gyrodactylus salaris \Jun. 2014 (Gsalaris_v1) \GCA_000715275.1 \net \ H. bacteriophora/m31e Heterorhabditis bacteriophora \Aug. 2011 (WS229/H. bacteriophora 7.0/hetBac1) \Aug. 2011 (WS229/H. bacteriophora 7.0/hetBac1) \net \ Haemonchus_contortus Haemonchus contortus \Aug. 2013 (HCON) \GCA_000469685.1 \net \ Heligmosomoides_polygyrus_bakeri Heligmosomoides polygyrus bakeri \Sep. 2016 (nHp_v2.0) \GCA_900096555.1 \net \ Heterodera_glycines Heterodera glycines \Apr. 2008 (HG2) \GCA_000150805.1 \net \ Hymenolepis_microstoma Hymenolepis microstoma \Dec. 2015 (HMIC002) \GCA_000469805.2 \net \ Loa_loa Loa loa \Jul. 2012 (Loa_loa_V3.1) \GCF_000183805.2 \net \ M. hapla Meloidogyne hapla \Sep. 2008 (M. hapla VW9 WS210/melHap1) \Sep. 2008 (M. hapla VW9 WS210/melHap1) \net \ M. incognita Meloidogyne incognita \Feb. 2008 (M. incognita WS245/PRJEA28837/melInc2) \Feb. 2008 (M. incognita WS245/PRJEA28837/melInc2) \net \ Macrostomum_lignano Macrostomum lignano \Aug. 2017 (Mlig_3_7) \GCA_002269645.1 \net \ Meloidogyne_arenaria Meloidogyne arenaria \May 2018 (ASM313380v1) \GCA_003133805.1 \net \ Meloidogyne_floridensis Meloidogyne floridensis \Jun. 2014 (nMf_1_1) \GCA_000751915.1 \net \ Meloidogyne_graminicola Meloidogyne graminicola \Nov. 2017 (Mgraminicola_V1) \GCA_002778205.1 \net \ Meloidogyne_incognita Meloidogyne incognita \May 2017 (Meloidogyne_incognita_V3) \GCA_900182535.1 \net \ Meloidogyne_javanica Meloidogyne javanica \Apr. 2017 (ASM90000394v1) \GCA_900003945.1 \net \ Microworm Panagrellus redivivus \Feb. 2013 (WS240/Pred3/panRed1) \Feb. 2013 (WS240/Pred3/panRed1) \net \ N. americanus Necator americanus \Dec. 2013 (WS242/N_americanus_v1/necAme1) \Dec. 2013 (WS242/N_americanus_v1/necAme1) \net \ Necator_americanus Necator americanus \Dec. 2013 (N_americanus_v1) \GCF_000507365.1 \net \ Nippostrongylus_brasiliensis Nippostrongylus brasiliensis \Aug. 2017 (NbL5_MIMR_Canu1.5) \GCA_900200055.1 \net \ O. volvulus Onchocerca volvulus \Nov. 2013 (WS241/O_volvulus_Cameroon_v3/oncVol1) \Nov. 2013 (WS241/O_volvulus_Cameroon_v3/oncVol1) \net \ Oesophagostomum_dentatum Oesophagostomum dentatum \Dec. 2014 (O_dentatum_10.0.ec.cg.pg) \GCA_000797555.1 \net \ Onchocerca_flexuosa Onchocerca flexuosa \Aug. 2017 (O_flexuosa_1.0.allpaths.pg.lrna) \GCA_002249935.1 \net \ Onchocerca_ochengi Onchocerca ochengi \Mar. 2016 (O_ochengi_Ngaoundere) \GCA_000950515.2 \net \ Onchocerca_volvulus Onchocerca volvulus \Feb. 2014 (ASM49940v2) \GCA_000499405.2 \net \ Opisthorchis_viverrini Opisthorchis viverrini \Jul. 2014 (OpiViv1.0) \GCA_000715545.1 \net \ Oscheius_MCB Oscheius sp. MCB \Feb. 2015 (ASM93487v1) \GCA_000934875.1 \net \ Oscheius_TEL_2014 Oscheius sp. TEL-2014 \Jan. 2016 (ASM151353v1) \GCA_001513535.1 \net \ Oscheius_tipulae Oscheius tipulae \May 2017 (Oscheius_tipulae_assembly_v2) \GCA_900184235.1 \net \ P. exspectatus Pristionchus exspectatus \Mar. 2014 (WS243/P_exspectatus_v1/priExs1) \Mar. 2014 (WS243/P_exspectatus_v1/priExs1) \net \ P. pacificus Pristionchus pacificus \Aug. 2014 (WS221/P_pacificus-v2/priPac3) \Aug. 2014 (WS221/P_pacificus-v2/priPac3) \net \ Parapristionchus_giblindavisi Parapristionchus giblindavisi \Jun. 2018 (Parapristionchus_genome) \GCA_900491355.1 \net \ Parascaris_univalens Parascaris univalens \Aug. 2017 (ASM225921v1) \GCA_002259215.1 \net \ Parastrongyloides_trichosuri Parastrongyloides trichosuri \Sep. 2014 (P_trichosuri_KNP) \GCA_000941615.1 \net \ Pig roundworm Ascaris suum \Sep. 2012 (WS229/AscSuum_1.0/ascSuu1) \Sep. 2012 (WS229/AscSuum_1.0/ascSuu1) \net \ Pine wood nematode Bursaphelenchus xylophilus \Nov. 2011 (WS229/B. xylophilus Ka4C1/burXyl1) \Nov. 2011 (WS229/B. xylophilus Ka4C1/burXyl1) \net \ Plectus_sambesii Plectus sambesii \Nov. 2017 (Psam_v1.0) \GCA_002796945.1 \net \ Pristionchus_arcanus Pristionchus arcanus \Jun. 2018 (P._arcanus_genome) \GCA_900490705.1 \net \ Pristionchus_entomophagus Pristionchus entomophagus \Jun. 2018 (P._entomophagus_genome) \GCA_900490825.1 \net \ Pristionchus_exspectatus Pristionchus exspectatus \May 2018 (Pristionchus_exspectatus_de_novo_assembly) \GCA_900380275.1 \net \ Pristionchus_maxplancki Pristionchus maxplancki \Jun. 2018 (Prisstionchus_maxplancki_genome) \GCA_900490775.1 \net \ Pristionchus_pacificus Pristionchus pacificus \Oct. 2017 (El_Paco) \GCA_000180635.3 \net \ Rhabditophanes_KR3021 Rhabditophanes sp. KR3021 \Sep. 2014 (Rhabditophanes_sp_KR3021) \GCA_000944355.1 \net \ Romanomermis_culicivorax Romanomermis culicivorax \Jan. 2014 (nRc.2.0) \GCA_001039655.1 \net \ Rotylenchulus_reniformis Rotylenchulus reniformis \Jun. 2015 (RREN1.0) \GCA_001026735.1 \net \ Schistosoma_haematobium Schistosoma haematobium \Jun. 2014 (SchHae_1.0) \GCA_000699445.1 \net \ Schistosoma_japonicum Schistosoma japonicum \Apr. 2009 (ASM15177v1) \GCA_000151775.1 \net \ Schistosoma_mansoni Schistosoma mansoni \Dec. 2011 (ASM23792v2) \GCA_000237925.2 \net \ Schmidtea_mediterranea Schmidtea mediterranea \Oct. 2017 (ASM260089v1) \GCA_002600895.1 \net \ Setaria_digitata Setaria digitata \Jan. 2018 (Sdigitata) \GCA_900083525.1 \net \ Setaria_equina Setaria equina \Mar. 2018 (Setequ3.0) \GCA_003012265.1 \net \ Spirometra_erinaceieuropaei Spirometra erinaceieuropaei \Sep. 2014 (S_erinaceieuropaei) \GCA_000951995.1 \net \ Steinernema_carpocapsae Steinernema carpocapsae \Sep. 2014 (S_carpo_v1) \GCA_000757645.1 \net \ Steinernema_feltiae Steinernema feltiae \Sep. 2014 (S_felt_v1) \GCA_000757705.1 \net \ Steinernema_glaseri Steinernema glaseri \Sep. 2014 (S_glas_v1) \GCA_000757755.1 \net \ Steinernema_monticolum Steinernema monticolum \Dec. 2013 (S_monti_v1) \GCA_000505645.1 \net \ Steinernema_scapterisci Steinernema scapterisci \Sep. 2014 (S_scapt_v1) \GCA_000757745.1 \net \ Strongyloides_papillosus Strongyloides papillosus \Nov. 2014 (S_papillosus_LIN) \GCA_000936265.1 \net \ Strongyloides_stercoralis Strongyloides stercoralis \Nov. 2014 (S_stercoralis_PV0001) \GCA_000947215.1 \net \ Strongyloides_venezuelensis Strongyloides venezuelensis \Jun. 2015 (S_venezuelensis_HH1) \GCA_001028725.1 \net \ Subanguina_moxae Subanguina moxae \Apr. 2015 (SAMX_assembly_v0.8) \GCA_000981365.1 \net \ Taenia_asiatica Taenia asiatica \Sep. 2016 (Taenia_asiatica_TASYD01_v1) \GCA_001693035.2 \net \ Taenia_multiceps Taenia multiceps \Jul. 2018 (T_multiceps_v2.0) \GCA_001923025.2 \net \ Taenia_saginata Taenia saginata \Oct. 2016 (ASM169307v2) \GCA_001693075.2 \net \ Taenia_solium Taenia solium \Nov. 2016 (MEX_genome_complete.1-6-13) \GCA_001870725.1 \net \ Teladorsagia_circumcincta Teladorsagia circumcincta \Sep. 2017 (T_circumcincta.14.0.ec.cg.pg) \GCA_002352805.1 \net \ Threadworm Strongyloides ratti \Sep. 2014 (S. ratti ED321/strRat2) \Sep. 2014 (S. ratti ED321/strRat2) \net \ Toxocara_canis Toxocara canis \Dec. 2014 (Toxocara_canis_adult_r1.0) \GCA_000803305.1 \net \ Trichinella Trichinella spiralis \Jan. 2011 (WS225/Trichinella_spiralis-3.7.1/triSpi1) \Jan. 2011 (WS225/Trichinella_spiralis-3.7.1/triSpi1) \net \ Trichinella_T6 Trichinella sp. T6 \Nov. 2015 (T6_ISS34_r1.0) \GCA_001447435.1 \net \ Trichinella_T8 Trichinella sp. T8 \Nov. 2015 (T8_ISS272_r1.0) \GCA_001447745.1 \net \ Trichinella_T9 Trichinella sp. T9 \Nov. 2015 (T9_ISS409_r1.0) \GCA_001447505.1 \net \ Trichinella_britovi Trichinella britovi \Nov. 2015 (T3_ISS120_r1.0) \GCA_001447585.1 \net \ Trichinella_murrelli Trichinella murrelli \Jul. 2017 (ASM222148v1) \GCA_002221485.1 \net \ Trichinella_nativa Trichinella nativa \Nov. 2015 (T2_ISS10_r1.0) \GCA_001447565.1 \net \ Trichinella_nelsoni Trichinella nelsoni \Nov. 2015 (T7_ISS37_r1.0) \GCA_001447455.1 \net \ Trichinella_papuae Trichinella papuae \Nov. 2015 (T10_ISS1980_r1.0) \GCA_001447755.1 \net \ Trichinella_patagoniensis Trichinella patagoniensis \Nov. 2015 (T12_ISS2496_r1.0) \GCA_001447655.1 \net \ Trichinella_pseudospiralis Trichinella pseudospiralis \Nov. 2015 (T4_ISS588_r1.0) \GCA_001447725.1 \net \ Trichinella_spiralis Trichinella spiralis \Jan. 2011 (Trichinella_spiralis-3.7.1) \GCF_000181795.1 \net \ Trichinella_zimbabwensis Trichinella zimbabwensis \Nov. 2015 (T11_ISS1029_r1.0) \GCA_001447665.1 \net \ Trichuris_muris Trichuris muris \Mar. 2014 (TMUE2.2) \GCA_000612645.1 \net \ Trichuris_trichiura Trichuris trichiura \Mar. 2014 (TTRE2.1) \GCA_000613005.1 \net \ Whipworm Trichuris suis \Jul. 2014 (WS243/T. suis DCEP-RM93M male/triSui1) \Jul. 2014 (WS243/T. suis DCEP-RM93M male/triSui1) \net \ Wuchereria_bancrofti Wuchereria bancrofti \Feb. 2016 (Wb_PNG_Genome_assembly_pt22) \GCA_001555675.1 \net
\ Table 1. Genome assemblies included in the 135-way Conservation track.\
\ The track configuration options allow the user to display the three different\ sets of scores by all, subclass, individually, or any combination of these.\ In full and pack display modes, conservation scores are displayed as a\ wiggle track (histogram) in which the height reflects the\ value of the score.\ The conservation wiggles can be configured in a variety of ways to\ highlight different aspects of the displayed information.\ Click the Graph configuration help link for an explanation\ of the configuration options.
\\ Pairwise alignments of each species to the C. elegans genome are\ displayed below the conservation histogram as a grayscale density plot (in\ pack mode) or as a wiggle (in full mode) that indicates alignment quality.\ In dense display mode, conservation is shown in grayscale using\ darker values to indicate higher levels of overall conservation\ as scored by phastCons.
\\ Checkboxes on the track configuration page allow selection of the\ species to include in the pairwise display.\ Configuration buttons are available to select all of the species\ (Set all), deselect all of the species (Clear all), or\ use the default settings (Set defaults).\ Note that excluding species from the pairwise display does not alter the\ the conservation score display.
\\ To view detailed information about the alignments at a specific\ position, zoom the display in to 30,000 or fewer bases, then click on\ the alignment.
\ \\ The Display chains between alignments configuration option\ enables display of gaps between alignment blocks in the pairwise alignments in\ a manner similar to the Chain track display. The following\ conventions are used:\
\ Discontinuities in the genomic context (chromosome, scaffold or region) of the\ aligned DNA in the aligning species are shown as follows:\
\ When zoomed-in to the base-level display, the track shows the base\ composition of each alignment.\ The numbers and symbols on the Gaps\ line indicate the lengths of gaps in the C. elegans sequence at those\ alignment positions relative to the longest non-C. elegans sequence.\ If there is sufficient space in the display, the size of the gap is shown.\ If the space is insufficient and the gap size is a multiple of 3, a\ "*" is displayed; other gap sizes are indicated by "+".
\\ Codon translation is available in base-level display mode if the\ displayed region is identified as a coding segment. To display this annotation,\ select the species for translation from the pull-down menu in the Codon\ Translation configuration section at the top of the page. Then, select one of\ the following modes:\
\ Codon translation uses the following gene tracks as the basis for\ translation, depending on the species chosen (Table 2).\ \
\ \\
\ Table 2. Gene tracks used for codon translation.\\ Gene Track Species \ Ensembl Genes v92 C. elegans, Ciona intestinalis \ WormBase WS245 genes C. angaria, C. japonica, C. briggsae, C. sp. 5 ju800, C. remanei, C. brenneri, C. tropicalis, P. exspectatus, P. pacificus, Pine wood nematode, N. americanus, A. ceylanicum, Pig roundworm, Barber pole worm, Whipworm, Microworm, Filarial worm, Dog heartworm, O. volvulus, Eye worm, M. incognita, M. hapla, H. bacteriophora/m31e, Trichinella \ \ no annotations all others
\ Pairwise alignments with the C. elegans genome were generated for\ each species using lastz from repeat-masked genomic sequence.\ Pairwise alignments were then linked into chains using a dynamic programming\ algorithm that finds maximally scoring chains of gapless subsections\ of the alignments organized in a kd-tree.\ Please note the specific parameters for the alignments.\ High-scoring chains were then placed along the genome, with\ gaps filled by lower-scoring chains, to produce an alignment net.\ For more information about the chaining and netting process and\ parameters for each species, see the description pages for the \ \ Chain and Net tracks.\
\\ The resulting best-in-genome pairwise alignments\ were progressively aligned using multiz/autoMZ,\ following the tree topology diagrammed above, to produce multiple alignments.\ The multiple alignments were post-processed to\ add annotations indicating alignment gaps, genomic breaks,\ and base quality of the component sequences.\ The annotated multiple alignments, in MAF format, are available for\ bulk download.\ An alignment summary table containing an entry for each\ alignment block in each species was generated to improve\ track display performance at large scales.\ Framing tables were constructed to enable\ visualization of codons in the multiple alignment display.
\ \\ Both phastCons and phyloP are phylogenetic methods that rely\ on a tree model containing the tree topology, branch lengths representing\ evolutionary distance at neutrally evolving sites, the background distribution\ of nucleotides, and a substitution rate matrix.\ The\ all species tree model for this track was\ generated using the phyloFit program from the PHAST package\ (REV model, EM algorithm, medium precision) using multiple alignments of\ 4-fold degenerate sites extracted from the 135-way alignment\ (msa_view). The 4d sites were derived from the NCBI RefSeq gene set,\ filtered to select single-coverage long transcripts.\
\\ This same tree model was used in the phyloP calculations, however their\ background frequencies were modified to maintain reversibility.\ The resulting tree model for\ all species.\
\\ The phastCons program computes conservation scores based on a phylo-HMM, a\ type of probabilistic model that describes both the process of DNA\ substitution at each site in a genome and the way this process changes from\ one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and\ Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for\ conserved regions and a state for non-conserved regions. The value plotted\ at each site is the posterior probability that the corresponding alignment\ column was "generated" by the conserved state of the phylo-HMM. These\ scores reflect the phylogeny (including branch lengths) of the species in\ question, a continuous-time Markov model of the nucleotide substitution\ process, and a tendency for conservation levels to be autocorrelated along\ the genome (i.e., to be similar at adjacent sites). The general reversible\ (REV) substitution model was used. Unlike many conservation-scoring programs,\ phastCons does not rely on a sliding window\ of fixed size; therefore, short highly-conserved regions and long moderately\ conserved regions can both obtain high scores.\ More information about\ phastCons can be found in Siepel et al. 2005.
\\ The phastCons parameters used were: expected-length=45,\ target-coverage=0.3, rho=0.3.
\ \\ The phyloP program supports several different methods for computing\ p-values of conservation or acceleration, for individual nucleotides or\ larger elements\ (\ http://compgen.cshl.edu/phast/).\ Here it was used\ to produce separate scores at each base (--wig-scores option), considering\ all branches of the phylogeny rather than a particular subtree or lineage\ (i.e., the --subtree option was not used). The scores were computed by\ performing a likelihood ratio test at each alignment column (--method LRT),\ and scores for both conservation and acceleration were produced (--mode CONACC).\
\\ The conserved elements were predicted by running phastCons with the\ --viterbi option. The predicted elements are segments of the alignment\ that are likely to have been "generated" by the conserved state of the\ phylo-HMM. Each element is assigned a log-odds score equal to its log\ probability under the conserved model minus its log probability under the\ non-conserved model. The "score" field associated with this track contains\ transformed log-odds scores, taking values between 0 and 1000. (The scores\ are transformed using a monotonic function of the form a * log(x) + b.) The\ raw log odds scores are retained in the "name" field and can be seen on the\ details page or in the browser when the track's display mode is set to\ "pack" or "full".\
\ \This track was created using the following programs:\
The phylogenetic tree is based on Murphy et al. (2001) and general\ consensus in the vertebrate phylogeny community as of March 2007.\
\ \\ Felsenstein J, Churchill GA.\ A Hidden Markov Model approach to\ variation among sites in rate of evolution.\ Mol Biol Evol. 1996 Jan;13(1):93-104.\ PMID: 8583911\
\ \\
Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A.\
\
Detection of nonneutral substitution rates on mammalian phylogenies.\
Genome Res. 2010 Jan;20(1):110-21.\
PMID: 19858363; PMC:
\
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K,\
Clawson H, Spieth J, Hillier LW, Richards S, et al.\
Evolutionarily conserved elements in vertebrate, insect, worm,\
and yeast genomes.\
Genome Res. 2005 Aug;15(8):1034-50.\
PMID: 16024819; PMC:
\ Siepel A, Haussler D.\ Phylogenetic Hidden Markov Models.\ In: Nielsen R, editor. Statistical Methods in Molecular Evolution.\ New York: Springer; 2005. pp. 325-351.\
\ \\
Yang Z.\
A space-time process model for the evolution of DNA\
sequences.\
Genetics. 1995 Feb;139(2):993-1005.\
PMID: 7713447; PMC:
\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes.\
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.\
PMID: 14500911; PMC:
\
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM,\
Baertsch R, Rosenbloom K, Clawson H, Green ED, et al.\
Aligning multiple genomic sequences with the threaded blockset aligner.\
Genome Res. 2004 Apr;14(4):708-15.\
PMID: 15060014; PMC:
\ Chiaromonte F, Yap VB, Miller W.\ Scoring pairwise genomic sequence alignments.\ Pac Symp Biocomput. 2002:115-26.\ PMID: 11928468\
\ \\ Harris RS.\ Improved pairwise alignment of genomic DNA.\ Ph.D. Thesis. Pennsylvania State University, USA. 2007.\
\ \\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
Human-mouse alignments with BLASTZ.\
Genome Res. 2003 Jan;13(1):103-7.\
PMID: 12529312; PMC:
\ Bernard G, Ragan MA, Chan CX.\ Recapitulating phylogenies using k-mers: from trees to networks.\ F1000Res. 2016;5:2789.\ PMID: 28105314\
\ \\ Fan H, Ives AR, Surget-Groba Y, Cannon CH.\ An assembly and alignment-free method of phylogeny reconstruction from \ next-generation sequencing data. BMC Genomics. 2015;16(1):522.\ PMID: 26169061\
\ \\ Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E,\ Ryder OA, Stanhope MJ, de Jong WW, Springer MS.\ Resolution of the early placental mammal radiation using Bayesian phylogenetics.\ Science. 2001 Dec 14;294(5550):2348-51.\ PMID: 11743200\
\ compGeno 1 compositeTrack on\ dragAndDrop subTracks\ group compGeno\ longLabel Multiz Alignment & Conservation (135 species: 112 nematodes, 22 flatworms and Ciona intestinalis)\ priority 2\ shortLabel Cons 135 species\ subGroup1 view Views align=Multiz_Alignments phyloP=Basewise_Conservation_(phyloP) phastcons=Element_Conservation_(phastCons) elements=Conserved_Elements\ track cons135way\ type bed 4\ visibility full\ cons135wayViewelements Conserved Elements bed 4 Multiz Alignment & Conservation (135 species: 112 nematodes, 22 flatworms and Ciona intestinalis) 1 2 0 0 0 127 127 127 0 0 0 compGeno 1 longLabel Multiz Alignment & Conservation (135 species: 112 nematodes, 22 flatworms and Ciona intestinalis)\ parent cons135way\ shortLabel Conserved Elements\ track cons135wayViewelements\ view elements\ visibility dense\ cons135wayViewphastcons Element Conservation (phastCons) bed 4 Multiz Alignment & Conservation (135 species: 112 nematodes, 22 flatworms and Ciona intestinalis) 2 2 0 0 0 127 127 127 0 0 0 compGeno 1 longLabel Multiz Alignment & Conservation (135 species: 112 nematodes, 22 flatworms and Ciona intestinalis)\ parent cons135way\ shortLabel Element Conservation (phastCons)\ track cons135wayViewphastcons\ view phastcons\ visibility full\ cons135wayViewalign Multiz Alignments bed 4 Multiz Alignment & Conservation (135 species: 112 nematodes, 22 flatworms and Ciona intestinalis) 3 2 0 0 0 127 127 127 0 0 0 compGeno 1 longLabel Multiz Alignment & Conservation (135 species: 112 nematodes, 22 flatworms and Ciona intestinalis)\ parent cons135way\ shortLabel Multiz Alignments\ track cons135wayViewalign\ view align\ viewUi on\ visibility pack\ refSeqComposite NCBI RefSeq genePred RefSeq genes from NCBI 1 2 0 0 0 127 127 127 0 0 0\ The NCBI RefSeq Genes composite track shows C. elegans protein-coding and non-protein-coding\ genes taken from the NCBI RNA reference sequences collection (RefSeq). All subtracks use\ coordinates provided by RefSeq, except for the UCSC RefSeq track, which UCSC produces by\ realigning the RefSeq RNAs to the genome. This realignment may result in occasional differences\ between the annotation coordinates provided by UCSC and NCBI. For RNA-seq analysis, we advise\ using NCBI aligned tables like RefSeq All or RefSeq Curated. See the \ Methods section for more details about how the different tracks were \ created.
\\ Please visit NCBI's Feedback for Gene and Reference Sequences (RefSeq) page to make suggestions, \ submit additions and corrections, or ask for help concerning RefSeq records.
\ \\ For more information on the different gene tracks, see our Genes FAQ.
\ \\ This track is a composite track that contains differing data sets.\ To show only a selected set of subtracks, uncheck the boxes next to the tracks that you wish to \ hide. Note: Not all subtracts are available on all assemblies.
\ \ The possible subtracks include:\\ The RefSeq All, RefSeq Curated, RefSeq Predicted, and\ UCSC RefSeq tracks follow the display conventions for\ gene prediction tracks.\ The color shading indicates the level of review the RefSeq record has undergone:\ predicted (light), provisional (medium), or reviewed (dark), as defined by RefSeq.
\ \\
| Color | \Level of review | \
|---|---|
| \ | Reviewed: the RefSeq record has been reviewed by NCBI staff or by a collaborator. The NCBI review process includes assessing available sequence data and the literature. Some RefSeq records may incorporate expanded sequence and annotation information. | \
| \ | Provisional: the RefSeq record has not yet been subject to individual review. The initial sequence-to-gene association has been established by outside collaborators or NCBI staff. | \
| \ | Predicted: the RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq record is predicted. | \
\ The item labels and codon display properties for features within this track can be configured \ through the check-box controls at the top of the track description page. To adjust the settings \ for an individual subtrack, click the wrench icon next to the track name in the subtrack list .
\The RefSeq Diffs track contains five different types of inconsistency between the\ reference genome sequence and the RefSeq transcript sequences. The five types of differences are\ as follows:\
\ When reporting HGVS with RefSeq sequences, to make sure that results from\ research articles can be mapped to the genome unambiguously, \ please specify the RefSeq annotation release displayed on the transcript's\ Genome Browser details page and also the RefSeq transcript ID with version\ (e.g. NM_012309.4 not NM_012309). \
\ \ \ \\ Tracks contained in the RefSeq annotation and RefSeq RNA alignment tracks were created at UCSC using \ data from the NCBI RefSeq project. Data files were downloaded from RefSeq in GFF file format and \ converted to the genePred and PSL table formats for display in the Genome Browser. Information about\ the NCBI annotation pipeline can be found \ here.
\ \The RefSeq Diffs track is generated by UCSC using NCBI's RefSeq RNA alignments.
\\ The UCSC RefSeq Genes track is constructed using the same methods as previous RefSeq Genes tracks.\ RefSeq RNAs were aligned against the C. elegans genome using BLAT. Those with an alignment of\ less than 15% were discarded. When a single RNA aligned in multiple places, the alignment\ having the highest base identity was identified. Only alignments having a base identity\ level within 0.1% of the best and at least 96% base identity with the genomic sequence were\ kept.
\ \\ The raw data for these tracks can be accessed in multiple ways. It can be explored interactively \ using the REST API,\ Table Browser or\ Data Integrator. The tables can also be accessed programmatically through our\ public MySQL server or downloaded from our\ downloads server for local processing. The previous track versions are available\ in the archives of our downloads server. You can also access any RefSeq table\ entries in JSON format through our \ JSON API.
\\ The data in the RefSeq Other and RefSeq Diffs tracks are organized in \ bigBed file format; more\ information about accessing the information in this bigBed file can be found\ below. The other subtracks are associated with database tables as follows:
\\ The first column of each of these tables is "bin". This column is designed\ to speed up access for display in the Genome Browser, but can be safely ignored in downstream\ analysis. You can read more about the bin indexing system\ here.
\\ The annotations in the RefSeqOther and RefSeqDiffs tracks are stored in bigBed \ files, which can be obtained from our downloads server here,\ ncbiRefSeqOther.bb and \ ncbiRefSeqDiffs.bb.\ Individual regions or the whole set of genome-wide annotations can be obtained using our tool\ bigBedToBed which can be compiled from the source code or downloaded as a precompiled\ binary for your system from the utilities directory linked below. For example, to extract only\ annotations in a given region, you could use the following command:
\\ bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/ce11/ncbiRefSeq/ncbiRefSeqOther.bb\ -chrom=chr16 -start=34990190 -end=36727467 stdout
\\ You can download a GTF format version of the RefSeq All table from the \ GTF downloads directory.\ The genePred format tracks can also be converted to GTF format using the\ genePredToGtf utility, available from the\ utilities directory on the UCSC downloads \ server. The utility can be run from the command line like so:
\ genePredToGtf ce11 ncbiRefSeqPredicted ncbiRefSeqPredicted.gtf\\ Note that using genePredToGtf in this manner accesses our public MySQL server, and you therefore \ must set up your hg.conf as described on the MySQL page linked near the beginning of the Data Access\ section.
\\ A file containing the RNA sequences in FASTA format for all items in the RefSeq All, RefSeq Curated, \ and RefSeq Predicted tracks can be found on our downloads server\ here.
\\ Please refer to our mailing list archives for questions.
\ \\ Previous versions of the ncbiRefSeq set of tracks can be found on our archive download server.\
\ \\ This track was produced at UCSC from data generated by scientists worldwide and curated by the\ NCBI RefSeq project.
\ \\
Kent WJ.\
BLAT - the BLAST-like \
alignment tool. Genome Res. 2002 Apr;12(4):656-64.\
PMID: 11932250; PMC:
\ Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J,\ Landrum MJ, McGarvey KM et al.\ RefSeq: an update on mammalian reference sequences.\ Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63.\ PMID: 24259432; PMC: \ PMC3965018
\\
Pruitt KD, Tatusova T, Maglott DR.\
\
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts \
and proteins.\
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4.\
PMID: 15608248; PMC:
CpG islands are associated with genes, particularly housekeeping\ genes, in vertebrates. CpG islands are typically common near\ transcription start sites and may be associated with promoter\ regions. Normally a C (cytosine) base followed immediately by a \ G (guanine) base (a CpG) is rare in\ vertebrate DNA because the Cs in such an arrangement tend to be\ methylated. This methylation helps distinguish the newly synthesized\ DNA strand from the parent strand, which aids in the final stages of\ DNA proofreading after duplication. However, over evolutionary time,\ methylated Cs tend to turn into Ts because of spontaneous\ deamination. The result is that CpGs are relatively rare unless\ there is selective pressure to keep them or a region is not methylated\ for some other reason, perhaps having to do with the regulation of gene\ expression. CpG islands are regions where CpGs are present at\ significantly higher levels than is typical for the genome as a whole.
\ \\ The unmasked version of the track displays potential CpG islands\ that exist in repeat regions and would otherwise not be visible\ in the repeat masked version.\
\ \\ By default, only the masked version of the track is displayed. To view the\ unmasked version, change the visibility settings in the track controls at\ the top of this page.\
\ \CpG islands were predicted by searching the sequence one base at a\ time, scoring each dinucleotide (+17 for CG and -1 for others) and\ identifying maximally scoring segments. Each segment was then\ evaluated for the following criteria:\ \
\ The entire genome sequence, masking areas included, was\ used for the construction of the track Unmasked CpG.\ The track CpG Islands is constructed on the sequence after\ all masked sequence is removed.\
\ \The CpG count is the number of CG dinucleotides in the island. \ The Percentage CpG is the ratio of CpG nucleotide bases\ (twice the CpG count) to the length. The ratio of observed to expected \ CpG is calculated according to the formula (cited in \ Gardiner-Garden et al. (1987)):\ \
Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)\ \ where N = length of sequence.\
\ The calculation of the track data is performed by the following command sequence:\
\
twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \\\
| cpg_lh /dev/stdin 2> cpg_lh.err \\\
| awk '{$2 = $2 - 1; width = $3 - $2; printf("%s\\t%d\\t%s\\t%s %s\\t%s\\t%s\\t%0.0f\\t%0.1f\\t%s\\t%s\\n", $1, $2, $3, $5, $6, width, $6, width*$7*0.01, 100.0*2*$6/width, $7, $9);}' \\\
| sort -k1,1 -k2,2n > cpgIsland.bed\
\
The unmasked track data is constructed from\
twoBitToFa -noMask output for the twoBitToFa command.\
\
\
\ CpG islands and its associated tables can be explored interactively using the\ REST API, the\ Table Browser or the\ Data Integrator.\ All the tables can also be queried directly from our public MySQL\ servers, with more information available on our\ help page as well as on\ our blog.
\\ The source for the cpg_lh program can be obtained from\ src/utils/cpgIslandExt/.\ The cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose "save file")\
\ \This track was generated using a modification of a program developed by G. Miklem and L. Hillier \ (unpublished).
\ \\ Gardiner-Garden M, Frommer M.\ \ CpG islands in vertebrate genomes.\ J Mol Biol. 1987 Jul 20;196(2):261-82.\ PMID: 3656447\
\ regulation 1 html cpgIslandSuper\ longLabel CpG Islands on All Sequence (Islands < 300 Bases are Light Green)\ parent cpgIslandSuper hide\ priority 2\ shortLabel Unmasked CpG\ track cpgIslandExtUnmasked\ netCaeRem4 caeRem4 Net netAlign caeRem4 chainCaeRem4 C. remanei (Jul. 2007 (WS220/caeRem4)) Alignment Net 1 3 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel C. remanei (Jul. 2007 (WS220/caeRem4)) Alignment Net\ otherDb caeRem4\ parent nematodesChainNetViewnet off\ shortLabel caeRem4 Net\ subGroups view=net species=s001 clade=c00\ track netCaeRem4\ type netAlign caeRem4 chainCaeRem4\ chainC_briggsae C_briggsae Chain chain C_briggsae C_briggsae (C_briggsae) Chained Alignments 3 4 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel C_briggsae (C_briggsae) Chained Alignments\ otherDb C_briggsae\ parent nematodesChainNetViewchain off\ shortLabel C_briggsae Chain\ subGroups view=chain species=s002 clade=c00\ track chainC_briggsae\ type chain C_briggsae\ phyloP26way 26 nematodes Cons wig -3.992 9.159 26 nematodes Basewise Conservation by PhyloP 2 4 60 60 140 140 60 60 0 0 0 compGeno 0 altColor 140,60,60\ autoScale off\ color 60,60,140\ configurable on\ longLabel 26 nematodes Basewise Conservation by PhyloP\ maxHeightPixels 100:50:11\ noInherit on\ parent cons26wayViewphyloP on\ priority 4\ shortLabel 26 nematodes Cons\ spanList 1\ subGroups view=phyloP\ track phyloP26way\ type wig -3.992 9.159\ viewLimits -1:4\ windowingFunction mean\ phyloP135way Cons 135 species wig -20 7.532 135 species Basewise Conservation by PhyloP 2 4 60 60 140 140 60 60 0 0 0 compGeno 0 altColor 140,60,60\ autoScale off\ color 60,60,140\ configurable on\ longLabel 135 species Basewise Conservation by PhyloP\ maxHeightPixels 100:50:11\ noInherit on\ parent cons135wayViewphyloP on\ priority 4\ shortLabel Cons 135 species\ spanList 1\ subGroups view=phyloP\ track phyloP135way\ type wig -20 7.532\ viewLimits -4.5:4.88\ windowingFunction mean\ chainC_sp26_LS_2015 C_sp26_LS_2015 Chain chain C_sp26_LS_2015 C_sp26_LS_2015 (C_sp26_LS_2015) Chained Alignments 3 5 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel C_sp26_LS_2015 (C_sp26_LS_2015) Chained Alignments\ otherDb C_sp26_LS_2015\ parent nematodesChainNetViewchain off\ shortLabel C_sp26_LS_2015 Chain\ subGroups view=chain species=s003 clade=c00\ track chainC_sp26_LS_2015\ type chain C_sp26_LS_2015\ ncbiRefSeqPsl RefSeq Alignments psl RefSeq Alignments of RNAs 1 5 0 0 0 127 127 127 0 0 0 genes 1 baseColorDefault diffCodons\ baseColorUseCds table ncbiRefSeqCds\ baseColorUseSequence extFile seqNcbiRefSeq extNcbiRefSeq\ color 0,0,0\ idXref ncbiRefSeqLink mrnaAcc name\ indelDoubleInsert on\ indelQueryInsert on\ longLabel RefSeq Alignments of RNAs\ parent refSeqComposite off\ pepTable ncbiRefSeqPepTable\ priority 5\ pslSequence no\ shortLabel RefSeq Alignments\ showCdsAllScales .\ showCdsMaxZoom 10000.0\ showDiffBasesAllScales .\ showDiffBasesMaxZoom 10000.0\ track ncbiRefSeqPsl\ type psl\ chainCaePb3 caePb3 Chain chain caePb3 C. brenneri (Nov. 2010 (C. brenneri 6.0.1b/caePb3)) Chained Alignments 3 6 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel C. brenneri (Nov. 2010 (C. brenneri 6.0.1b/caePb3)) Chained Alignments\ otherDb caePb3\ parent nematodesChainNetViewchain off\ shortLabel caePb3 Chain\ subGroups view=chain species=s004 clade=c00\ track chainCaePb3\ type chain caePb3\ netCaePb3 caePb3 Net netAlign caePb3 chainCaePb3 C. brenneri (Nov. 2010 (C. brenneri 6.0.1b/caePb3)) Alignment Net 1 7 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel C. brenneri (Nov. 2010 (C. brenneri 6.0.1b/caePb3)) Alignment Net\ otherDb caePb3\ parent nematodesChainNetViewnet off\ shortLabel caePb3 Net\ subGroups view=net species=s004 clade=c00\ track netCaePb3\ type netAlign caePb3 chainCaePb3\ refGene UCSC RefSeq genePred refPep refMrna UCSC annotations of RefSeq RNAs (NM_* and NR_*) 3 7 12 12 120 133 133 187 0 0 0\ The RefSeq Genes track shows known C. elegans protein-coding and \ non-protein-coding genes taken from the NCBI RNA reference sequences \ collection (RefSeq). The data underlying this track are updated weekly.
\ \\ Please visit the Feedback for Gene and Reference Sequences (RefSeq) page to\ make suggestions, submit additions and corrections, or ask for help concerning\ RefSeq records.\
\ \\ This track follows the display conventions for \ gene prediction \ tracks.\ The color shading indicates the level of review the RefSeq record has \ undergone: predicted (light), provisional (medium), reviewed (dark). \
\ The item labels and display colors of features within this track can be\ configured through the controls at the top of the track description page. \ This page is accessed via the small button to the left of the track's \ graphical display or through the link on the track's control menu. \
\ RefSeq RNAs were aligned against the C. elegans genome using blat; \ those with an alignment of less than 15% were discarded. When a single RNA \ aligned in multiple places, the alignment having the highest base identity \ was identified. Only alignments having a base identity level within 0.1% of \ the best and at least 96% base identity with the genomic sequence were kept.\
\ \\ This track was produced at UCSC from RNA sequence data\ generated by scientists worldwide and curated by the \ NCBI RefSeq project.
\ \\
Kent WJ.\
\
BLAT - the BLAST-like alignment tool.\
Genome Res. 2002 Apr;12(4):656-64.\
PMID: 11932250; PMC:
\
Pruitt KD, Tatusova T, Maglott DR.\
\
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.\
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4.\
PMID: 15608248; PMC:
\ These gene predictions were generated by WormBase.\
\ \\ These gene predictions were produced and hand-curated by WormBase.\ For a detailed description of the methods, refer to\ Howe et al. (2016) in the References section below.\
\ \\ Thanks to WormBase for providing this annotation.\
\ \\
Howe KL, Bolt BJ, Cain S, Chan J, Chen WJ, Davis P, Done J, Down T, Gao S, Grove C et al.\
\
WormBase 2016: expanding to enable helminth genomic research.\
Nucleic Acids Res. 2016 Jan 4;44(D1):D774-80.\
PMID: 26578572; PMC:
\ This track shows alignments between C. elegans expressed sequence tags\ (ESTs) in GenBank and the genome that show signs of splicing when\ aligned against the genome. ESTs are single-read sequences, typically about \ 500 bases in length, that usually represent fragments of transcribed genes.\
\\ To be considered spliced, an EST must show \ evidence of at least one canonical intron, i.e. one that is at least\ 32 bases in length and has GT/AG ends. By requiring splicing, the level \ of contamination in the EST databases is drastically reduced\ at the expense of eliminating many genuine 3' ESTs.\ For a display of all ESTs (including unspliced), see the \ C. elegans EST track.
\ \\ This track follows the display conventions for \ PSL alignment tracks. In dense display mode, darker shading\ indicates a larger number of aligned ESTs.
\\ The strand information (+/-) indicates the\ direction of the match between the EST and the matching\ genomic sequence. It bears no relationship to the direction\ of transcription of the RNA with which it might be associated.
\\ The description page for this track has a filter that can be used to change \ the display mode, alter the color, and include/exclude a subset of items \ within the track. This may be helpful when many items are shown in the track \ display, especially when only some are relevant to the current task.
\\ To use the filter:\
\ This track may also be configured to display base labeling, a feature that\ allows the user to display all bases in the aligning sequence or only those \ that differ from the genomic sequence. For more information about this option,\ go to the Base Coloring for Alignment Tracks page.
\ \\ To make an EST, RNA is isolated from cells and reverse\ transcribed into cDNA. Typically, the cDNA is cloned\ into a plasmid vector and a read is taken from the 5'\ and/or 3' primer. For most — but not all — ESTs, the\ reverse transcription is primed by an oligo-dT, which\ hybridizes with the poly-A tail of mature mRNA. The\ reverse transcriptase may or may not make it to the 5'\ end of the mRNA, which may or may not be degraded.
\\ In general, the 3' ESTs mark the end of transcription\ reasonably well, but the 5' ESTs may end at any point\ within the transcript. Some of the newer cap-selected\ libraries cover transcription start reasonably well. Before the \ cap-selection techniques\ emerged, some projects used random rather than poly-A\ priming in an attempt to retrieve sequence distant from the\ 3' end. These projects were successful at this, but as\ a side effect also deposited sequences from unprocessed\ mRNA and perhaps even genomic sequences into the EST databases.\ Even outside of the random-primed projects, there is a\ degree of non-mRNA contamination. Because of this, a\ single unspliced EST should be viewed with considerable\ skepticism.
\\ To generate this track, C. elegans ESTs from GenBank were aligned \ against the genome using blat. Note that the maximum intron length\ allowed by blat is 750,000 bases, which may eliminate some ESTs with very \ long introns that might otherwise align. When a single \ EST aligned in multiple places, the alignment having the \ highest base identity was identified. Only alignments having\ a base identity level within 0.5% of the best and at least 96% base identity \ with the genomic sequence are displayed in this track.
\ \\ This track was produced at UCSC from EST sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.\
GenBank: update.\
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.\
PMID: 14681350; PMC:
\
Kent WJ.\
BLAT - the BLAST-like alignment tool.\
Genome Res. 2002 Apr;12(4):656-64.\
PMID: 11932250; PMC:
\ This track shows alignments between C. elegans expressed sequence tags\ (ESTs) in GenBank and the genome. ESTs are single-read sequences, \ typically about 500 bases in length, that usually represent fragments of \ transcribed genes.
\ \\ This track follows the display conventions for \ PSL alignment tracks. In dense display mode, the items that\ are more darkly shaded indicate matches of better quality.
\\ The strand information (+/-) indicates the\ direction of the match between the EST and the matching\ genomic sequence. It bears no relationship to the direction\ of transcription of the RNA with which it might be associated.
\\ The description page for this track has a filter that can be used to change \ the display mode, alter the color, and include/exclude a subset of items \ within the track. This may be helpful when many items are shown in the track \ display, especially when only some are relevant to the current task.
\\ To use the filter:\
\ This track may also be configured to display base labeling, a feature that\ allows the user to display all bases in the aligning sequence or only those \ that differ from the genomic sequence. For more information about this option,\ go to the Base Coloring for Alignment Tracks page.
\ \\ To make an EST, RNA is isolated from cells and reverse\ transcribed into cDNA. Typically, the cDNA is cloned\ into a plasmid vector and a read is taken from the 5'\ and/or 3' primer. For most — but not all — ESTs, the\ reverse transcription is primed by an oligo-dT, which\ hybridizes with the poly-A tail of mature mRNA. The\ reverse transcriptase may or may not make it to the 5'\ end of the mRNA, which may or may not be degraded.
\\ In general, the 3' ESTs mark the end of transcription\ reasonably well, but the 5' ESTs may end at any point\ within the transcript. Some of the newer cap-selected\ libraries cover transcription start reasonably well. Before the \ cap-selection techniques\ emerged, some projects used random rather than poly-A\ priming in an attempt to retrieve sequence distant from the\ 3' end. These projects were successful at this, but as\ a side effect also deposited sequences from unprocessed\ mRNA and perhaps even genomic sequences into the EST databases.\ Even outside of the random-primed projects, there is a\ degree of non-mRNA contamination. Because of this, a\ single unspliced EST should be viewed with considerable\ skepticism.
\\ To generate this track, C. elegans ESTs from GenBank were aligned \ against the genome using blat. Note that the maximum intron length\ allowed by blat is 750,000 bases, which may eliminate some ESTs with very \ long introns that might otherwise align. When a single \ EST aligned in multiple places, the alignment having the \ highest base identity was identified. Only alignments having\ a base identity level within 0.5% of the best and at least 96% base identity \ with the genomic sequence were kept.
\ \\ This track was produced at UCSC from EST sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.\
GenBank: update.\
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.\
PMID: 14681350; PMC:
\
Kent WJ.\
BLAT - the BLAST-like alignment tool.\
Genome Res. 2002 Apr;12(4):656-64.\
PMID: 11932250; PMC:
\ The mRNA track shows alignments between C. elegans mRNAs\ in GenBank and the genome.
\ \\ This track follows the display conventions for \ PSL alignment tracks. In dense display mode, the items that\ are more darkly shaded indicate matches of better quality.
\\ The description page for this track has a filter that can be used to change \ the display mode, alter the color, and include/exclude a subset of items \ within the track. This may be helpful when many items are shown in the track \ display, especially when only some are relevant to the current task.
\\ To use the filter:\
\ This track may also be configured to display codon coloring, a feature that\ allows the user to quickly compare mRNAs against the genomic sequence. For more \ information about this option, go to the\ Codon and Base Coloring for Alignment Tracks page.
\ \\ GenBank C. elegans mRNAs were aligned against the genome using the \ blat program. When a single mRNA aligned in multiple places, \ the alignment having the highest base identity was found. \ Only alignments having a base identity level within 0.5% of\ the best and at least 96% base identity with the genomic sequence were kept.\
\ \\ The mRNA track was produced at UCSC from mRNA sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.\
GenBank: update.\
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.\
PMID: 14681350; PMC:
\
Kent WJ.\
BLAT - the BLAST-like alignment tool.\
Genome Res. 2002 Apr;12(4):656-64.\
PMID: 11932250; PMC:
\ This track shows the sequences used in the Aug. 2014 C. elegans genome assembly.\
\\
Genome assembly procedures are covered in the NCBI\
assembly documentation.
\
NCBI also provides\
specific information about this assembly.\
\ The definition of this assembly is from the\ AGP file delivered with the sequence. The NCBI document\ AGP Specification describes the format of the AGP file.\
\\ In dense mode, this track depicts the contigs that make up the \ currently viewed scaffold. \ Contig boundaries are distinguished by the use of alternating gold and brown \ coloration. Where gaps\ exist between contigs, spaces are shown between the gold and brown\ blocks. The relative order and orientation of the contigs\ within a scaffold is always known; therefore, a line is drawn in the graphical\ display to bridge the blocks.
\\ Component types found in this track (with counts of that type in parentheses):\
\ This track shows ab initio predictions from the program\ AUGUSTUS (version 3.1).\ The predictions are based on the genome sequence alone.\
\ \\ For more information on the different gene tracks, see our Genes FAQ.
\ \\ Statistical signal models were built for splice sites, branch-point\ patterns, translation start sites, and the poly-A signal.\ Furthermore, models were built for the sequence content of\ protein-coding and non-coding regions as well as for the length distributions\ of different exon and intron types. Detailed descriptions of most of these different models\ can be found in Mario Stanke's\ dissertation.\ This track shows the most likely gene structure according to a\ Semi-Markov Conditional Random Field model.\ Alternative splicing transcripts were obtained with\ a sampling algorithm (--alternatives-from-sampling=true --sample=100 --minexonintronprob=0.2\ --minmeanexonintronprob=0.5 --maxtracks=3 --temperature=2).\
\ \\ The different models used by Augustus were trained on a number of different species-specific\ gene sets, which included 1000-2000 training gene structures. The --species option allows\ one to choose the species used for training the models. Different training species were used\ for the --species option when generating these predictions for different groups of\ assemblies.\
| Assembly Group | \ \ \Training Species | \ \
| Fish | \ \ \zebrafish\ \ |
| Birds | \ \ \chicken\ \ |
| Human and all other vertebrates | \ \ \human\ \ |
| Nematodes | \ \ \caenorhabditis | \ \
| Drosophila | \ \ \fly | \ \
| A. mellifera | \ \ \honeybee1 | \ \
| A. gambiae | \ \ \culex | \ \
| S. cerevisiae | \ \ \saccharomyces | \ \
\ This table describes which training species was used for a particular group of assemblies.\ When available, the closest related training species was used.\
\ \\ Stanke M, Diekhans M, Baertsch R, Haussler D.\ \ Using native and syntenically mapped cDNA alignments to improve de novo gene finding.\ Bioinformatics. 2008 Mar 1;24(5):637-44.\ PMID: 18218656\
\ \\ Stanke M, Waack S.\ \ Gene prediction with a hidden Markov model and a new intron submodel.\ Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25.\ PMID: 14534192\
\ genes 1 baseColorDefault genomicCodons\ baseColorUseCds given\ color 12,105,0\ group genes\ longLabel AUGUSTUS ab initio gene predictions v3.1\ shortLabel AUGUSTUS\ track augustusGene\ type genePred\ visibility hide\ nematodesChainNetViewchain Chains bed 3 Nematodes Chain and Net Alignments 3 100 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Nematodes Chain and Net Alignments\ parent nematodesChainNet\ shortLabel Chains\ spectrum on\ track nematodesChainNetViewchain\ view chain\ visibility pack\ cytoBandIdeo Chromosome Band (Ideogram) bed 4 + Ideogram for Orientation 1 100 0 0 0 127 127 127 0 0 0 map 1 group map\ longLabel Ideogram for Orientation\ shortLabel Chromosome Band (Ideogram)\ track cytoBandIdeo\ type bed 4 +\ visibility dense\ cpgIslandSuper CpG Islands bed 4 + CpG Islands (Islands < 300 Bases are Light Green) 0 100 0 100 0 128 228 128 0 0 0CpG islands are associated with genes, particularly housekeeping\ genes, in vertebrates. CpG islands are typically common near\ transcription start sites and may be associated with promoter\ regions. Normally a C (cytosine) base followed immediately by a \ G (guanine) base (a CpG) is rare in\ vertebrate DNA because the Cs in such an arrangement tend to be\ methylated. This methylation helps distinguish the newly synthesized\ DNA strand from the parent strand, which aids in the final stages of\ DNA proofreading after duplication. However, over evolutionary time,\ methylated Cs tend to turn into Ts because of spontaneous\ deamination. The result is that CpGs are relatively rare unless\ there is selective pressure to keep them or a region is not methylated\ for some other reason, perhaps having to do with the regulation of gene\ expression. CpG islands are regions where CpGs are present at\ significantly higher levels than is typical for the genome as a whole.
\ \\ The unmasked version of the track displays potential CpG islands\ that exist in repeat regions and would otherwise not be visible\ in the repeat masked version.\
\ \\ By default, only the masked version of the track is displayed. To view the\ unmasked version, change the visibility settings in the track controls at\ the top of this page.\
\ \CpG islands were predicted by searching the sequence one base at a\ time, scoring each dinucleotide (+17 for CG and -1 for others) and\ identifying maximally scoring segments. Each segment was then\ evaluated for the following criteria:\ \
\ The entire genome sequence, masking areas included, was\ used for the construction of the track Unmasked CpG.\ The track CpG Islands is constructed on the sequence after\ all masked sequence is removed.\
\ \The CpG count is the number of CG dinucleotides in the island. \ The Percentage CpG is the ratio of CpG nucleotide bases\ (twice the CpG count) to the length. The ratio of observed to expected \ CpG is calculated according to the formula (cited in \ Gardiner-Garden et al. (1987)):\ \
Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)\ \ where N = length of sequence.\
\ The calculation of the track data is performed by the following command sequence:\
\
twoBitToFa assembly.2bit stdout | maskOutFa stdin hard stdout \\\
| cpg_lh /dev/stdin 2> cpg_lh.err \\\
| awk '{$2 = $2 - 1; width = $3 - $2; printf("%s\\t%d\\t%s\\t%s %s\\t%s\\t%s\\t%0.0f\\t%0.1f\\t%s\\t%s\\n", $1, $2, $3, $5, $6, width, $6, width*$7*0.01, 100.0*2*$6/width, $7, $9);}' \\\
| sort -k1,1 -k2,2n > cpgIsland.bed\
\
The unmasked track data is constructed from\
twoBitToFa -noMask output for the twoBitToFa command.\
\
\
\ CpG islands and its associated tables can be explored interactively using the\ REST API, the\ Table Browser or the\ Data Integrator.\ All the tables can also be queried directly from our public MySQL\ servers, with more information available on our\ help page as well as on\ our blog.
\\ The source for the cpg_lh program can be obtained from\ src/utils/cpgIslandExt/.\ The cpg_lh program binary can be obtained from: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh (choose "save file")\
\ \This track was generated using a modification of a program developed by G. Miklem and L. Hillier \ (unpublished).
\ \\ Gardiner-Garden M, Frommer M.\ \ CpG islands in vertebrate genomes.\ J Mol Biol. 1987 Jul 20;196(2):261-82.\ PMID: 3656447\
\ regulation 1 altColor 128,228,128\ color 0,100,0\ group regulation\ html cpgIslandSuper\ longLabel CpG Islands (Islands < 300 Bases are Light Green)\ shortLabel CpG Islands\ superTrack on\ track cpgIslandSuper\ type bed 4 +\ crispr CRISPR bed 3 CRISPR/Cas9 Sp. Pyog. target sites 0 100 0 0 0 127 127 127 0 0 0\ This track shows regions of the genome within 200 bp of transcribed regions and\ DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme\ from S. pyogenes (PAM: NGG).\ CRISPR target sites were annotated with predicted specificity\ (off-target effects) and predicted efficiency (on-target cleavage) by various\ algorithms through the tool CRISPOR.\
\ \\ The track "CRISPR Regions" shows the regions of the genome where target\ sites were analyzed, i.e. within 200 bp of transcribed regions as annotated by\ Ensembl transcript models.
\ \\ The track "CRISPR Targets" shows the target sites in these regions.\ The target sequence of the guide is shown with a thick (exon) bar. The PAM\ motif match (NGG) is shown with a thinner bar. Guides\ are colored to reflect both predicted specificity and efficiency. Specificity\ reflects the "uniqueness" of a 20mer sequence in the genome; the less unique a\ sequence is, the more likely it is to cleave other locations of the genome\ (off-target effects). Efficiency is the frequency of cleavage at the target\ site (on-target efficiency).
\ \Shades of gray stand for sites that are hard to target specifically, as the\ 20mer is not very unique in the genome:
\| impossible to target: target site has at least one identical copy in the genome and was not scored | |
| hard to target: many similar sequences in the genome that alignment stopped, repeat? | |
| hard to target: target site was aligned but results in a low specificity score <= 50 (see below) |
Colors highlight targets that are specific in the genome (MIT specificity > 50) but have different predicted efficiencies:
\| unable to calculate Doench/Fusi 2016 efficiency score | |
| low predicted cleavage: Doench/Fusi 2016 Efficiency percentile <= 30 | |
| medium predicted cleavage: Doench/Fusi 2016 Efficiency percentile > 30 and < 55 | |
| high predicted cleavage: Doench/Fusi 2016 Efficiency > 55 |
\
Mouse-over a target site to show predicted specificity and efficiency scores:
\
Click onto features to show all scores and predicted off-targets with up to\ four mismatches. The Out-of-Frame score by Bae et al. 2014\ is correlated with\ the probability that mutations induced by the guide RNA will disrupt the open\ reading frame. The authors recommend out-of-frame scores > 66 to create\ knock-outs with a single guide efficiently.
\ \
Off-target sites are sorted by the CFD (Cutting Frequency Determination) \ score (Doench et al. 2016). \ The higher the CFD score, the more likely there is off-target cleavage at that site. \ Off-targets with a CFD score < 0.023 are not shown on this page, but are availble when \ following the link to the external CRISPOR tool. \ When compared against experimentally validated off-targets by \ Haeussler et al. 2016, the large majority of predicted\ off-targets with CFD scores < 0.023 were false-positives.
\ \\ Like most algorithms, the MIT specificity score is not always a perfect\ predictor of off-target effects. Despite low scores, many tested guides \ caused few and/or weak off-target cleavage when tested with whole-genome assays\ (Figure 2 from Haeussler\ et al. 2016), as shown below, and the published data contains few data points\ with high specificity scores. Overall though, the assays showed that the higher\ the specificity score, the lower the off-target effects.
\ \
\
\
Similarly, efficiency scoring is not very accurate: guides with low\ scores can be efficient and vice versa. As a general rule, however, the higher\ the score, the less likely that a guide is very inefficient. The\ following histograms illustrate, for each type of score, how the share of\ inefficient guides drops with increasing efficiency scores:\
\ \
\
\
When reading this plot, keep in mind that both scores were evaluated on\ their own training data. Especially for the Moreno-Mateos score, the\ results are too optimistic, due to overfitting. When evaluated on independent\ datasets, the correlation of the prediction with other assays was around 25%\ lower, see Haeussler et al. 2016. At the time of\ writing, there is no independent dataset available yet to determine the\ Moreno-Mateos accuracy for each score percentile range.
\ \\
Exons as predicted by Ensembl Gene models were used, extended by 200 basepairs\
on each side, searched for the -NGG motif. Flanking 20mer guide sequences were\
aligned to the genome with BWA and scored with MIT Specificity scores using the\
command-line version of crispor.org. Non-unique guide sequences were skipped.\
Flanking sequences were extracted from the genome and input for Crispor\
efficiency scoring, available from the
\ The raw data can be explored interactively with the Table Browser.\ For automated analysis, the genome annotation is stored in a bigBed file that\ can be downloaded from\ our download server.\ The files for this track are called crispr.bb and crisprDetails.tab and are located in the /gbdb/ce11/crispr directory of our downloads server. Individual\ regions or the whole genome annotation can be obtained using our tool bigBedToBed,\ which can be compiled from the source code or downloaded as a precompiled\ binary for your system. Instructions for downloading source code and binaries can be found\ here. The tool\ can also be used to obtain only features within a given range, e.g. bigBedToBed\ http://hgdownload.soe.ucsc.edu/gbdb/hg19/crispr/crispr.bb -chrom=chr21\ -start=0 -end=10000000 stdout
\ \\ The file crisprDetails.tab includes the details of the off-targets. The last\ column of the bigBed file is the offset of the respective line in\ crisprDetails.tab. E.g. if the last column is 14227033723, then the following\ command will extract the line with the corresponding off-target details:\ curl -s -r 14227033723-14227043723 http://hgdownload.soe.ucsc.edu/gbdb/hg19/crispr/crisprDetails.tab | head -n1. The off-target details can currently not be joined with the table\ browser.
\ \\ The file crisprDetails.tab is a tab-separated text file with two fields. The\ first field contains the numbers of off-targets for each mismatch, e.g. "0,0,1,3,49" \ means 0 off-targets at zero mismatches, 1 at two mismatches, 3 at three and 49\ off-targets at four mismatches. The second field is a pipe-separated list of\ semicolon-separated tuples with the genome coordinates and the CFD score. E.g.\ "chr10;123376795+;42|chr5;148353274-;39" describes two off-targets, with the\ first at chr1:123376795 on the positive strand and a CFD score 0.42
\ \\ Track created by Maximilian Haeussler and Hiram Clawson, with helpful input from Jean-Paul Concordet (MNHN Paris) and Alberto Stolfi (NYU).\
\ \\
Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud JB, Schneider-Maunoury S,\
Shkumatava A, Teboul L, Kent J et al.\
Evaluation of off-target and on-target scoring algorithms and integration into the\
guide RNA selection tool CRISPOR.\
Genome Biol. 2016 Jul 5;17(1):148.\
PMID: 27380939; PMC:
\ Bae S, Kweon J, Kim HS, Kim JS.\ \ Microhomology-based choice of Cas9 nuclease target sites.\ Nat Methods. 2014 Jul;11(7):705-6.\ PMID: 24972169\
\ \\
Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C,\
Orchard R et al.\
\
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9.\
Nat Biotechnol. 2016 Feb;34(2):184-91.\
PMID: 26780180; PMC:
\
Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O\
et al.\
\
DNA targeting specificity of RNA-guided Cas9 nucleases.\
Nat Biotechnol. 2013 Sep;31(9):827-32.\
PMID: 23873081; PMC:
\
Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ.\
\
CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo.\
Nat Methods. 2015 Oct;12(10):982-8.\
PMID: 26322839; PMC:
\ This track shows regions of the genome within 200 bp of transcribed regions and\ DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme\ from S. pyogenes (PAM: NGG).\ CRISPR target sites were annotated with predicted specificity\ (off-target effects) and predicted efficiency (on-target cleavage) by various\ algorithms through the tool CRISPOR.\
\ \\ The track "CRISPR Regions" shows the regions of the genome where target\ sites were analyzed, i.e. within 200 bp of transcribed regions as annotated by\ Ensembl transcript models.
\ \\ The track "CRISPR Targets" shows the target sites in these regions.\ The target sequence of the guide is shown with a thick (exon) bar. The PAM\ motif match (NGG) is shown with a thinner bar. Guides\ are colored to reflect both predicted specificity and efficiency. Specificity\ reflects the "uniqueness" of a 20mer sequence in the genome; the less unique a\ sequence is, the more likely it is to cleave other locations of the genome\ (off-target effects). Efficiency is the frequency of cleavage at the target\ site (on-target efficiency).
\ \Shades of gray stand for sites that are hard to target specifically, as the\ 20mer is not very unique in the genome:
\| impossible to target: target site has at least one identical copy in the genome and was not scored | |
| hard to target: many similar sequences in the genome that alignment stopped, repeat? | |
| hard to target: target site was aligned but results in a low specificity score <= 50 (see below) |
Colors highlight targets that are specific in the genome (MIT specificity > 50) but have different predicted efficiencies:
\| unable to calculate Doench/Fusi 2016 efficiency score | |
| low predicted cleavage: Doench/Fusi 2016 Efficiency percentile <= 30 | |
| medium predicted cleavage: Doench/Fusi 2016 Efficiency percentile > 30 and < 55 | |
| high predicted cleavage: Doench/Fusi 2016 Efficiency > 55 |
\
Mouse-over a target site to show predicted specificity and efficiency scores:
\
Click onto features to show all scores and predicted off-targets with up to\ four mismatches. The Out-of-Frame score by Bae et al. 2014\ is correlated with\ the probability that mutations induced by the guide RNA will disrupt the open\ reading frame. The authors recommend out-of-frame scores > 66 to create\ knock-outs with a single guide efficiently.
\ \
Off-target sites are sorted by the CFD (Cutting Frequency Determination) \ score (Doench et al. 2016). \ The higher the CFD score, the more likely there is off-target cleavage at that site. \ Off-targets with a CFD score < 0.023 are not shown on this page, but are availble when \ following the link to the external CRISPOR tool. \ When compared against experimentally validated off-targets by \ Haeussler et al. 2016, the large majority of predicted\ off-targets with CFD scores < 0.023 were false-positives.
\ \\ Like most algorithms, the MIT specificity score is not always a perfect\ predictor of off-target effects. Despite low scores, many tested guides \ caused few and/or weak off-target cleavage when tested with whole-genome assays\ (Figure 2 from Haeussler\ et al. 2016), as shown below, and the published data contains few data points\ with high specificity scores. Overall though, the assays showed that the higher\ the specificity score, the lower the off-target effects.
\ \\
\
Similarly, efficiency scoring is not very accurate: guides with low\ scores can be efficient and vice versa. As a general rule, however, the higher\ the score, the less likely that a guide is very inefficient. The\ following histograms illustrate, for each type of score, how the share of\ inefficient guides drops with increasing efficiency scores:\
\ \\
\
When reading this plot, keep in mind that both scores were evaluated on\ their own training data. Especially for the Moreno-Mateos score, the\ results are too optimistic, due to overfitting. When evaluated on independent\ datasets, the correlation of the prediction with other assays was around 25%\ lower, see Haeussler et al. 2016. At the time of\ writing, there is no independent dataset available yet to determine the\ Moreno-Mateos accuracy for each score percentile range.
\ \\
Exons as predicted by Ensembl Gene models were used, extended by 200 basepairs\
on each side, searched for the -NGG motif. Flanking 20mer guide sequences were\
aligned to the genome with BWA and scored with MIT Specificity scores using the\
command-line version of crispor.org. Non-unique guide sequences were skipped.\
Flanking sequences were extracted from the genome and input for Crispor\
efficiency scoring, available from the
\ The raw data can be explored interactively with the Table Browser.\ For automated analysis, the genome annotation is stored in a bigBed file that\ can be downloaded from\ our download server.\ The files for this track are called crispr.bb and crisprDetails.tab and are located in the /gbdb/ce11/crispr directory of our downloads server. Individual\ regions or the whole genome annotation can be obtained using our tool bigBedToBed,\ which can be compiled from the source code or downloaded as a precompiled\ binary for your system. Instructions for downloading source code and binaries can be found\ here. The tool\ can also be used to obtain only features within a given range, e.g. bigBedToBed\ http://hgdownload.soe.ucsc.edu/gbdb/hg19/crisprRanges/crispr.bb -chrom=chr21\ -start=0 -end=10000000 stdout
\ \\ The file crisprDetails.tab includes the details of the off-targets. The last\ column of the bigBed file is the offset of the respective line in\ crisprDetails.tab. E.g. if the last column is 14227033723, then the following\ command will extract the line with the corresponding off-target details:\ curl -s -r 14227033723-14227043723 http://hgdownload.soe.ucsc.edu/gbdb/hg19/crispr/crisprDetails.tab | head -n1. The off-target details can currently not be joined with the table\ browser.
\ \\ The file crisprDetails.tab is a tab-separated text file with two fields. The\ first field contains the numbers of off-targets for each mismatch, e.g. "0,0,1,3,49" \ means 0 off-targets at zero mismatches, 1 at two mismatches, 3 at three and 49\ off-targets at four mismatches. The second field is a pipe-separated list of\ semicolon-separated tuples with the genome coordinates and the CFD score. E.g.\ "chr10;123376795+;42|chr5;148353274-;39" describes two off-targets, with the\ first at chr1:123376795 on the positive strand and a CFD score 0.42
\ \\ Track created by Maximilian Haeussler and Hiram Clawson, with helpful input from Jean-Paul Concordet (MNHN Paris) and Alberto Stolfi (NYU).\
\ \\
Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud JB, Schneider-Maunoury S,\
Shkumatava A, Teboul L, Kent J et al.\
Evaluation of off-target and on-target scoring algorithms and integration into the\
guide RNA selection tool CRISPOR.\
Genome Biol. 2016 Jul 5;17(1):148.\
PMID: 27380939; PMC:
\ Bae S, Kweon J, Kim HS, Kim JS.\ \ Microhomology-based choice of Cas9 nuclease target sites.\ Nat Methods. 2014 Jul;11(7):705-6.\ PMID: 24972169\
\ \\
Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C,\
Orchard R et al.\
\
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9.\
Nat Biotechnol. 2016 Feb;34(2):184-91.\
PMID: 26780180; PMC:
\
Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O\
et al.\
\
DNA targeting specificity of RNA-guided Cas9 nucleases.\
Nat Biotechnol. 2013 Sep;31(9):827-32.\
PMID: 23873081; PMC:
\
Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ.\
\
CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo.\
Nat Methods. 2015 Oct;12(10):982-8.\
PMID: 26322839; PMC:
\ This track shows regions of the genome within 200 bp of transcribed regions and\ DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme\ from S. pyogenes (PAM: NGG).\ CRISPR target sites were annotated with predicted specificity\ (off-target effects) and predicted efficiency (on-target cleavage) by various\ algorithms through the tool CRISPOR.\
\ \\ The track "CRISPR Regions" shows the regions of the genome where target\ sites were analyzed, i.e. within 200 bp of transcribed regions as annotated by\ Ensembl transcript models.
\ \\ The track "CRISPR Targets" shows the target sites in these regions.\ The target sequence of the guide is shown with a thick (exon) bar. The PAM\ motif match (NGG) is shown with a thinner bar. Guides\ are colored to reflect both predicted specificity and efficiency. Specificity\ reflects the "uniqueness" of a 20mer sequence in the genome; the less unique a\ sequence is, the more likely it is to cleave other locations of the genome\ (off-target effects). Efficiency is the frequency of cleavage at the target\ site (on-target efficiency).
\ \Shades of gray stand for sites that are hard to target specifically, as the\ 20mer is not very unique in the genome:
\| impossible to target: target site has at least one identical copy in the genome and was not scored | |
| hard to target: many similar sequences in the genome that alignment stopped, repeat? | |
| hard to target: target site was aligned but results in a low specificity score <= 50 (see below) |
Colors highlight targets that are specific in the genome (MIT specificity > 50) but have different predicted efficiencies:
\| unable to calculate Doench/Fusi 2016 efficiency score | |
| low predicted cleavage: Doench/Fusi 2016 Efficiency percentile <= 30 | |
| medium predicted cleavage: Doench/Fusi 2016 Efficiency percentile > 30 and < 55 | |
| high predicted cleavage: Doench/Fusi 2016 Efficiency > 55 |
\
Mouse-over a target site to show predicted specificity and efficiency scores:
\
Click onto features to show all scores and predicted off-targets with up to\ four mismatches. The Out-of-Frame score by Bae et al. 2014\ is correlated with\ the probability that mutations induced by the guide RNA will disrupt the open\ reading frame. The authors recommend out-of-frame scores > 66 to create\ knock-outs with a single guide efficiently.
\ \
Off-target sites are sorted by the CFD (Cutting Frequency Determination) \ score (Doench et al. 2016). \ The higher the CFD score, the more likely there is off-target cleavage at that site. \ Off-targets with a CFD score < 0.023 are not shown on this page, but are availble when \ following the link to the external CRISPOR tool. \ When compared against experimentally validated off-targets by \ Haeussler et al. 2016, the large majority of predicted\ off-targets with CFD scores < 0.023 were false-positives.
\ \\ Like most algorithms, the MIT specificity score is not always a perfect\ predictor of off-target effects. Despite low scores, many tested guides \ caused few and/or weak off-target cleavage when tested with whole-genome assays\ (Figure 2 from Haeussler\ et al. 2016), as shown below, and the published data contains few data points\ with high specificity scores. Overall though, the assays showed that the higher\ the specificity score, the lower the off-target effects.
\ \\
\
Similarly, efficiency scoring is not very accurate: guides with low\ scores can be efficient and vice versa. As a general rule, however, the higher\ the score, the less likely that a guide is very inefficient. The\ following histograms illustrate, for each type of score, how the share of\ inefficient guides drops with increasing efficiency scores:\
\ \\
\
When reading this plot, keep in mind that both scores were evaluated on\ their own training data. Especially for the Moreno-Mateos score, the\ results are too optimistic, due to overfitting. When evaluated on independent\ datasets, the correlation of the prediction with other assays was around 25%\ lower, see Haeussler et al. 2016. At the time of\ writing, there is no independent dataset available yet to determine the\ Moreno-Mateos accuracy for each score percentile range.
\ \\
Exons as predicted by Ensembl Gene models were used, extended by 200 basepairs\
on each side, searched for the -NGG motif. Flanking 20mer guide sequences were\
aligned to the genome with BWA and scored with MIT Specificity scores using the\
command-line version of crispor.org. Non-unique guide sequences were skipped.\
Flanking sequences were extracted from the genome and input for Crispor\
efficiency scoring, available from the
\ The raw data can be explored interactively with the Table Browser.\ For automated analysis, the genome annotation is stored in a bigBed file that\ can be downloaded from\ our download server.\ The files for this track are called crispr.bb and crisprDetails.tab and are located in the /gbdb/ce11/crispr directory of our downloads server. Individual\ regions or the whole genome annotation can be obtained using our tool bigBedToBed,\ which can be compiled from the source code or downloaded as a precompiled\ binary for your system. Instructions for downloading source code and binaries can be found\ here. The tool\ can also be used to obtain only features within a given range, e.g. bigBedToBed\ http://hgdownload.soe.ucsc.edu/gbdb/hg19/crisprTargets/crispr.bb -chrom=chr21\ -start=0 -end=10000000 stdout
\ \\ The file crisprDetails.tab includes the details of the off-targets. The last\ column of the bigBed file is the offset of the respective line in\ crisprDetails.tab. E.g. if the last column is 14227033723, then the following\ command will extract the line with the corresponding off-target details:\ curl -s -r 14227033723-14227043723 http://hgdownload.soe.ucsc.edu/gbdb/hg19/crispr/crisprDetails.tab | head -n1. The off-target details can currently not be joined with the table\ browser.
\ \\ The file crisprDetails.tab is a tab-separated text file with two fields. The\ first field contains the numbers of off-targets for each mismatch, e.g. "0,0,1,3,49" \ means 0 off-targets at zero mismatches, 1 at two mismatches, 3 at three and 49\ off-targets at four mismatches. The second field is a pipe-separated list of\ semicolon-separated tuples with the genome coordinates and the CFD score. E.g.\ "chr10;123376795+;42|chr5;148353274-;39" describes two off-targets, with the\ first at chr1:123376795 on the positive strand and a CFD score 0.42
\ \\ Track created by Maximilian Haeussler and Hiram Clawson, with helpful input from Jean-Paul Concordet (MNHN Paris) and Alberto Stolfi (NYU).\
\ \\
Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud JB, Schneider-Maunoury S,\
Shkumatava A, Teboul L, Kent J et al.\
Evaluation of off-target and on-target scoring algorithms and integration into the\
guide RNA selection tool CRISPOR.\
Genome Biol. 2016 Jul 5;17(1):148.\
PMID: 27380939; PMC:
\ Bae S, Kweon J, Kim HS, Kim JS.\ \ Microhomology-based choice of Cas9 nuclease target sites.\ Nat Methods. 2014 Jul;11(7):705-6.\ PMID: 24972169\
\ \\
Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C,\
Orchard R et al.\
\
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9.\
Nat Biotechnol. 2016 Feb;34(2):184-91.\
PMID: 26780180; PMC:
\
Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O\
et al.\
\
DNA targeting specificity of RNA-guided Cas9 nucleases.\
Nat Biotechnol. 2013 Sep;31(9):827-32.\
PMID: 23873081; PMC:
\
Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ.\
\
CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo.\
Nat Methods. 2015 Oct;12(10):982-8.\
PMID: 26322839; PMC:
\ These gene predictions were generated by Ensembl.\
\ \\ For more information on the different gene tracks, see our Genes FAQ.
\ \\ For a description of the methods used in Ensembl gene predictions, please refer to\ Hubbard et al. (2002), also listed in the References section below. \
\ \\
Ensembl Gene data can be explored interactively using the\
Table Browser or the\
Data Integrator. \
For local downloads, the genePred format files for ce11 are available in our\
\
downloads directory as ensGene.txt.gz or in our\
\
genes download directory in GTF format.
\
For programmatic access, the data can be queried from the \
REST API or\
directly from our public MySQL\
servers. Instructions on this method are available on our\
MySQL help page and on\
our blog.
\ Previous versions of this track can be found on our archive download server.\
\ \\ We would like to thank Ensembl for providing these gene annotations. For more information, please see\ Ensembl's genome annotation page.\
\ \\
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J,\
Curwen V, Down T et al.\
The Ensembl genome database project.\
Nucleic Acids Res. 2002 Jan 1;30(1):38-41.\
PMID: 11752248; PMC:
\ This track shows the gaps in the Aug. 2014 C. elegans genome assembly.\
\\
Genome assembly procedures are covered in the NCBI\
assembly documentation.
\
NCBI also provides\
specific information about this assembly.\
\ The definition of the gaps in this assembly is from the\ AGP file delivered with the sequence. The NCBI document\ AGP Specification describes the format of the AGP file.\
\\ Gaps are represented as black boxes in this track.\ If the relative order and orientation of the contigs on either side\ of the gap is supported by read pair data, \ it is a bridged gap and a white line is drawn \ through the black box representing the gap. \
\This assembly contains the following principal types of gaps:\
\ The GC percent track shows the percentage of G (guanine) and C (cytosine) bases\ in 5-base windows. High GC content is typically associated with\ gene-rich areas.\
\\ This track may be configured in a variety of ways to highlight different\ apsects of the displayed information. Click the\ "Graph configuration help"\ link for an explanation of the configuration options.\ \
The data and presentation of this graph were prepared by\ Hiram Clawson.\
\ \ map 0 altColor 128,128,128\ autoScale Off\ color 0,0,0\ graphTypeDefault Bar\ gridDefault OFF\ group map\ html gc5Base\ longLabel GC Percent in 5-Base Windows\ maxHeightPixels 128:36:16\ shortLabel GC Percent\ track gc5BaseBw\ type bigWig 0 100\ viewLimits 30:70\ visibility hide\ windowingFunction Mean\ genscan Genscan Genes genePred genscanPep Genscan Gene Predictions 0 100 170 100 0 212 177 127 0 0 0\ This track shows predictions from the\ Genscan program\ written by Chris Burge.\ The predictions are based on transcriptional, translational and donor/acceptor\ splicing signals as well as the length and compositional distributions of exons,\ introns and intergenic regions.\
\ \\ For more information on the different gene tracks, see our Genes FAQ.
\ \\ This track follows the display conventions for\ gene prediction\ tracks.\
\ \\ The track description page offers the following filter and configuration\ options:\
\ For a description of the Genscan program and the model that underlies it,\ refer to Burge and Karlin (1997) in the References section below.\ The splice site models used are described in more detail in Burge (1998)\ below.\
\ \\ Burge C.\ Modeling Dependencies in Pre-mRNA Splicing Signals.\ In: Salzberg S, Searls D, Kasif S, editors.\ Computational Methods in Molecular Biology.\ Amsterdam: Elsevier Science; 1998. p. 127-163.\
\ \\ Burge C, Karlin S.\ \ Prediction of complete gene structures in human genomic DNA.\ J. Mol. Biol. 1997 Apr 25;268(1):78-94.\ PMID: 9149143\
\ genes 1 color 170,100,0\ group genes\ longLabel Genscan Gene Predictions\ shortLabel Genscan Genes\ track genscan\ type genePred genscanPep\ visibility hide\ ucscToINSDC INSDC bed 4 Accession at INSDC - International Nucleotide Sequence Database Collaboration 0 100 0 0 0 127 127 127 0 0 0 https://www.ncbi.nlm.nih.gov/nuccore/$$\ This track associates UCSC Genome Browser chromosome names to accession\ names from the International Nucleotide Sequence Database Collaboration (INSDC).\
\ \\ The data were downloaded from the NCBI assembly database.\
\ \The data for this track was prepared by\ Hiram Clawson.\ \ map 1 group map\ longLabel Accession at INSDC - International Nucleotide Sequence Database Collaboration\ shortLabel INSDC\ track ucscToINSDC\ type bed 4\ url https://www.ncbi.nlm.nih.gov/nuccore/$$\ urlLabel INSDC link:\ visibility hide\ nestedRepeats Interrupted Rpts bed 12 + Fragments of Interrupted Repeats Joined by RepeatMasker ID 0 100 0 0 0 127 127 127 1 0 0
\ This track shows joined fragments of interrupted repeats extracted\ from the output of the \ RepeatMasker program which screens DNA sequences\ for interspersed repeats and low complexity DNA sequences using the\ \ Repbase Update library of repeats from the\ Genetic\ Information Research Institute (GIRI). Repbase Update is described in\ Jurka (2000) in the References section below.\
\ \\ The detailed annotations from RepeatMasker are in the RepeatMasker track. This\ track shows fragments of original repeat insertions which have been interrupted\ by insertions of younger repeats or through local rearrangements. The fragments\ are joined using the ID column of RepeatMasker output.\
\ \\ In pack or full mode, each interrupted repeat is displayed as boxes\ (fragments) joined by horizontal lines, labeled with the repeat name.\ If all fragments are on the same strand, arrows are added to the\ horizontal line to indicate the strand. In dense or squish mode, labels\ and arrows are omitted and in dense mode, all items are collapsed to\ fit on a single row.\
\ \\ Items are shaded according to the average identity score of their\ fragments. Usually, the shade of an item is similar to the shades of\ its fragments unless some fragments are much more diverged than\ others. The score displayed above is the average identity score,\ clipped to a range of 50% - 100% and then mapped to the range\ 0 - 1000 for shading in the browser.\
\ \\ UCSC has used the most current versions of the RepeatMasker software\ and repeat libraries available to generate these data. Note that these\ versions may be newer than those that are publicly available on the Internet.\
\ \\ Data are generated using the RepeatMasker -s flag. Additional flags\ may be used for certain organisms. See the\ FAQ for more information.\
\ \\ Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and\ repeat libraries used to generate this track.\
\ \\ Smit AFA, Hubley R, Green P.\ RepeatMasker Open-3.0.\ \ http://www.repeatmasker.org. 1996-2010.\
\ \\ Repbase Update is described in:\
\ \\ Jurka J.\ \ Repbase Update: a database and an electronic journal of repetitive elements.\ Trends Genet. 2000 Sep;16(9):418-420.\ PMID: 10973072\
\ \\ For a discussion of repeats in mammalian genomes, see:\
\ \\ Smit AF.\ \ Interspersed repeats and other mementos of transposable elements in mammalian genomes.\ Curr Opin Genet Dev. 1999 Dec;9(6):657-63.\ PMID: 10607616\
\ \\ Smit AF.\ \ The origin of interspersed repeats in the human genome.\ Curr Opin Genet Dev. 1996 Dec;6(6):743-8.\ PMID: 8994846\
\ varRep 1 exonNumbers off\ group varRep\ longLabel Fragments of Interrupted Repeats Joined by RepeatMasker ID\ shortLabel Interrupted Rpts\ track nestedRepeats\ type bed 12 +\ useScore 1\ visibility hide\ multiz135way Multiz Align wigMaf 0.0 1.0 Multiz Alignments of 135 species 3 100 0 10 100 0 90 10 0 0 0 compGeno 1 altColor 0,90,10\ color 0, 10, 100\ defaultMaf multiz135wayDefault\ frames multiz135wayFrames\ group compGeno\ irows on\ itemFirstCharCase noChange\ longLabel Multiz Alignments of 135 species\ noInherit on\ parent cons135wayViewalign on\ priority 100\ sGroup_Deuterostomia ci3\ sGroup_Dorylaimia Trichinella_murrelli Trichinella_zimbabwensis Trichinella_pseudospiralis Trichinella_papuae Trichinella_T6 Trichinella_britovi Trichinella_T8 Trichinella_T9 Trichinella_patagoniensis Trichinella_nelsoni Trichinella_nativa Trichinella_spiralis Romanomermis_culicivorax Trichuris_trichiura Trichuris_muris triSui1 triSpi1\ sGroup_Platyhelminthes Schmidtea_mediterranea Girardia_tigrina Dugesia_japonica Macrostomum_lignano Schistosoma_mansoni Schistosoma_haematobium Schistosoma_japonicum Gyrodactylus_salaris Hymenolepis_microstoma Fasciola_hepatica Taenia_multiceps Fasciola_gigantica Taenia_saginata Clonorchis_sinensis Opisthorchis_viverrini Echinococcus_multilocularis Taenia_asiatica Echinococcus_canadensis Taenia_solium Echinococcus_granulosus Spirometra_erinaceieuropaei Dicrocoelium_dendriticum\ sGroup_Plectida Plectus_sambesii\ sGroup_Rhabditina C_nigoni caeRem4 C_briggsae C_sp26_LS_2015 caePb3 C_latens caeSp111 C_sp34_TK_2017 C_sp40_LS_2015 caeJap4 C_sp39_LS_2015 C_sp38_MB_2015 C_sp31_LS_2015 caeSp51 caeAng2 cb4 C_sp32_LS_2015 Diploscapter_coronatus Diploscapter_pachys C_sp21_LS_2015 Ancylostoma_caninum Oscheius_tipulae ancCey1 Parapristionchus_giblindavisi Necator_americanus Oscheius_TEL_2014 Ancylostoma_duodenale Oesophagostomum_dentatum Pristionchus_arcanus Pristionchus_pacificus Pristionchus_maxplancki Pristionchus_entomophagus Pristionchus_exspectatus hetBac1 necAme1 Oscheius_MCB priPac3 priExs1\ sGroup_Spirurina Onchocerca_volvulus Wuchereria_bancrofti Dirofilaria_immitis Brugia_pahangi Onchocerca_ochengi Brugia_malayi Loa_loa Setaria_digitata Onchocerca_flexuosa Setaria_equina Ascaris_suum Parascaris_univalens Toxocara_canis ascSuu1 oncVol1 bruMal2 loaLoa1 dirImm1 Elaeophora_elaphi\ sGroup_Strongylida Dictyocaulus_viviparus Nippostrongylus_brasiliensis Heligmosomoides_polygyrus_bakeri Teladorsagia_circumcincta Haemonchus_contortus Angiostrongylus_cantonensis haeCon2\ sGroup_Tylenchina strRat2 Strongyloides_stercoralis Strongyloides_venezuelensis Meloidogyne_arenaria Strongyloides_papillosus Parastrongyloides_trichosuri Meloidogyne_incognita Meloidogyne_javanica Acrobeloides_nanus Rhabditophanes_KR3021 Meloidogyne_graminicola Rotylenchulus_reniformis Ditylenchus_destructor Bursaphelenchus_xylophilus Steinernema_monticolum Meloidogyne_floridensis Steinernema_carpocapsae Steinernema_scapterisci Steinernema_feltiae Subanguina_moxae Globodera_ellingtonae Globodera_rostochiensis Steinernema_glaseri Globodera_pallida Heterodera_glycines panRed1 burXyl1 melHap1 melInc2\ shortLabel Multiz Align\ speciesCodonDefault ce11\ speciesDefaultOff C_nigoni C_briggsae C_sp26_LS_2015 caePb3 C_latens caeSp111 C_sp34_TK_2017 C_sp40_LS_2015 caeJap4 C_sp39_LS_2015 C_sp38_MB_2015 C_sp31_LS_2015 caeSp51 caeAng2 C_sp32_LS_2015 Diploscapter_coronatus Diploscapter_pachys C_sp21_LS_2015 Ancylostoma_caninum Oscheius_tipulae Parapristionchus_giblindavisi Necator_americanus Oscheius_TEL_2014 Ancylostoma_duodenale Oesophagostomum_dentatum Pristionchus_arcanus Pristionchus_pacificus Pristionchus_maxplancki Pristionchus_entomophagus Pristionchus_exspectatus hetBac1 necAme1 Oscheius_MCB priExs1 Onchocerca_volvulus Wuchereria_bancrofti Dirofilaria_immitis Brugia_pahangi Onchocerca_ochengi Brugia_malayi Loa_loa Setaria_digitata Onchocerca_flexuosa Setaria_equina Ascaris_suum Parascaris_univalens Toxocara_canis oncVol1 bruMal2 loaLoa1 dirImm1 Elaeophora_elaphi Strongyloides_stercoralis Strongyloides_venezuelensis Meloidogyne_arenaria Strongyloides_papillosus Parastrongyloides_trichosuri Meloidogyne_incognita Meloidogyne_javanica Acrobeloides_nanus Rhabditophanes_KR3021 Meloidogyne_graminicola Rotylenchulus_reniformis Ditylenchus_destructor Bursaphelenchus_xylophilus Steinernema_monticolum Meloidogyne_floridensis Steinernema_carpocapsae Steinernema_scapterisci Steinernema_feltiae Subanguina_moxae Globodera_ellingtonae Globodera_rostochiensis Steinernema_glaseri Globodera_pallida Heterodera_glycines panRed1 melHap1 melInc2 Dictyocaulus_viviparus Nippostrongylus_brasiliensis Heligmosomoides_polygyrus_bakeri Teladorsagia_circumcincta Haemonchus_contortus Angiostrongylus_cantonensis haeCon2 Plectus_sambesii Trichinella_murrelli Trichinella_zimbabwensis Trichinella_pseudospiralis Trichinella_papuae Trichinella_T6 Trichinella_britovi Trichinella_T8 Trichinella_T9 Trichinella_patagoniensis Trichinella_nelsoni Trichinella_nativa Trichinella_spiralis Romanomermis_culicivorax Trichuris_trichiura Trichuris_muris triSpi1 Schmidtea_mediterranea Girardia_tigrina Dugesia_japonica Macrostomum_lignano Schistosoma_mansoni Schistosoma_haematobium Schistosoma_japonicum Gyrodactylus_salaris Hymenolepis_microstoma Fasciola_hepatica Taenia_multiceps Fasciola_gigantica Taenia_saginata Clonorchis_sinensis Opisthorchis_viverrini Echinococcus_multilocularis Taenia_asiatica Echinococcus_canadensis Taenia_solium Echinococcus_granulosus Spirometra_erinaceieuropaei Dicrocoelium_dendriticum ci3\ speciesDefaultOn caeRem4 cb4 ancCey1 priPac3 ascSuu1 strRat2 burXyl1 triSui1\ speciesGroups Rhabditina Spirurina Tylenchina Strongylida Plectida Dorylaimia Platyhelminthes Deuterostomia\ subGroups view=align\ summary multiz135waySummary\ track multiz135way\ treeImage phylo/ce11_135way.png\ type wigMaf 0.0 1.0\ multiz26way Multiz Align wigMaf 0.0 1.0 Multiz Alignments of 26 nematode assemblies 3 100 0 10 100 0 90 10 0 0 0 compGeno 1 altColor 0,90,10\ color 0, 10, 100\ frames multiz26wayFrames\ group compGeno\ irows on\ itemFirstCharCase noChange\ longLabel Multiz Alignments of 26 nematode assemblies\ noInherit on\ parent cons26wayViewalign on\ priority 100\ sGroup_Caenorhabditis caeSp51 caePb3 caeRem4 cb4 caeSp111 caeJap4 caeAng2\ sGroup_Others priExs1 priPac3 burXyl1 ancCey1 haeCon2 necAme1 panRed1 hetBac1 ascSuu1 strRat2 triSpi1 triSui1 melInc2 melHap1 bruMal2 oncVol1 loaLoa1 dirImm1\ shortLabel Multiz Align\ speciesCodonDefault ce11\ speciesGroups Caenorhabditis Others\ subGroups view=align\ summary multiz26waySummary\ track multiz26way\ treeImage phylo/ce11_26way.png\ type wigMaf 0.0 1.0\ nematodesChainNet Nematodes Chain/Net bed 3 Nematodes Chain and Net Alignments 0 100 0 0 0 255 255 0 0 0 0\ This track shows regions of the genome that are alignable\ to other genomes ("chain" subtracks) or in synteny ("net" subtracks).\ The alignable parts are shown with thick blocks that look like exons. \ Non-alignable parts between these are shown like introns.\
\ \\ The chain track shows alignments of a query genome sequence to the\ C. elegans genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ the query sequence and C. elegans simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ the query sequence assembly or an insertion in the C. elegans \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the C. elegans genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \\ The net track shows the best query sequence/C. elegans chain for \ every part of the C. elegans genome. It is useful for\ finding syntenic regions, possibly orthologs, and for studying genome\ rearrangement.
\ \By default, the chains to chromosome-based assemblies are colored\ based on which chromosome they map to in the aligning organism. To turn\ off the coloring, check the "off" button next to: Color\ track based on chromosome.
\\ To display only the chains of one chromosome in the aligning\ organism, enter the name of that chromosome (e.g. chr4) in box next to: \ Filter by chromosome.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\
Transposons that have been inserted since the query sequence/C. elegans\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single query sequence chromosome and a single\
C. elegans chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
\
\
Chains scoring below a minimum score of "5000" were discarded;\
the remaining chains are displayed in this track. The linear gap\
matrix used with axtChain:
\
-linearGap=loose\ \ tablesize 11\ smallSize 111\ position 1 2 3 11 111 2111 12111 32111 72111 152111 252111\ qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600\ tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600\ bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000\\ \ \
\ Chains were derived from lastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ Lastz (previously known as blastz) was developed at\ Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his \ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains and nets were created\ by Robert Baertsch and Jim Kent.
\\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ \
\ Chiaromonte F, Yap VB, Miller W.\ Scoring pairwise genomic sequence alignments.\ Pac Symp Biocomput. 2002:115-26.\ PMID: 11928468\
\ \\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes.\
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.\
PMID: 14500911; PMC:
\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
Human-mouse alignments with BLASTZ.\
Genome Res. 2003 Jan;13(1):103-7.\
PMID: 12529312; PMC:
\ This track displays translated blat alignments of vertebrate and\ invertebrate mRNA in \ GenBank from organisms other than C. elegans.\ \
\ This track follows the display conventions for \ PSL alignment tracks. In dense display mode, the items that\ are more darkly shaded indicate matches of better quality.
\\ The strand information (+/-) for this track is in two parts. The\ first + indicates the orientation of the query sequence whose\ translated protein produced the match (here always 5' to 3', hence +).\ The second + or - indicates the orientation of the matching \ translated genomic sequence. Because the two orientations of a DNA \ sequence give different predicted protein sequences, there are four \ combinations. ++ is not the same as --, nor is +- the same as -+.
\\ The description page for this track has a filter that can be used to change \ the display mode, alter the color, and include/exclude a subset of items \ within the track. This may be helpful when many items are shown in the track \ display, especially when only some are relevant to the current task.
\\ To use the filter:\
\ This track may also be configured to display codon coloring, a feature that\ allows the user to quickly compare mRNAs against the genomic sequence. For more \ information about this option, go to the\ Codon and Base Coloring for Alignment Tracks page.
\ \\ The mRNAs were aligned against the C. elegans genome using translated \ blat. When a single mRNA aligned in multiple places, the alignment having the \ highest base identity was found. Only those alignments having a base \ identity level within 1% of the best and at least 25% base identity with the \ genomic sequence were kept.
\ \\ The mRNA track was produced at UCSC from mRNA sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.\
GenBank: update.\
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.\
PMID: 14681350; PMC:
\
Kent WJ.\
BLAT - the BLAST-like alignment tool.\
Genome Res. 2002 Apr;12(4):656-64.\
PMID: 11932250; PMC:
\ This track shows known protein-coding and non-protein-coding genes \ for organisms other than C. elegans, taken from the NCBI RNA reference \ sequences collection (RefSeq). The data underlying this track are \ updated weekly.
\ \\ This track follows the display conventions for \ gene prediction \ tracks.\ The color shading indicates the level of review the RefSeq record has \ undergone: predicted (light), provisional (medium), reviewed (dark).
\\ The item labels and display colors of features within this track can be\ configured through the controls at the top of the track description page. \
\ The RNAs were aligned against the C. elegans genome using blat; those\ with an alignment of less than 15% were discarded. When a single RNA aligned \ in multiple places, the alignment having the highest base identity was \ identified. Only alignments having a base identity level within 0.5% of \ the best and at least 25% base identity with the genomic sequence were kept.\
\ \\ This track was produced at UCSC from RNA sequence data\ generated by scientists worldwide and curated by the \ NCBI RefSeq project.
\ \\
Kent WJ.\
\
BLAT--the BLAST-like alignment tool.\
Genome Res. 2002 Apr;12(4):656-64.\
PMID: 11932250; PMC:
\
Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J,\
Landrum MJ, McGarvey KM et al.\
\
RefSeq: an update on mammalian reference sequences.\
Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63.\
PMID: 24259432; PMC:
\
Pruitt KD, Tatusova T, Maglott DR.\
\
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.\
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4.\
PMID: 15608248; PMC:
\ This track associates UCSC Genome Browser chromosome names to accession\ identifiers from the NCBI Reference Sequence Database (RefSeq).\
\ \\ The data were downloaded from the NCBI assembly database.\
\ \The data for this track was prepared by\ Hiram Clawson.\ map 1 group map\ longLabel RefSeq Accession\ shortLabel RefSeq Acc\ track ucscToRefSeq\ type bed 4\ url https://www.ncbi.nlm.nih.gov/nuccore/$$\ urlLabel RefSeq accession:\ visibility hide\ simpleRepeat Simple Repeats bed 4 + Simple Tandem Repeats by TRF 0 100 0 0 0 127 127 127 0 0 0
\ This track displays simple tandem repeats (possibly imperfect repeats) located\ by Tandem Repeats\ Finder (TRF) which is specialized for this purpose. These repeats can\ occur within coding regions of genes and may be quite\ polymorphic. Repeat expansions are sometimes associated with specific\ diseases.
\ \\ For more information about the TRF program, see Benson (1999).\
\ \\ TRF was written by \ Gary Benson.
\ \\
Benson G.\
\
Tandem repeats finder: a program to analyze DNA sequences.\
Nucleic Acids Res. 1999 Jan 15;27(2):573-80.\
PMID: 9862982; PMC:
\ This track depicts masked sequence as determined by\ WindowMasker. The\ WindowMasker tool is included in the NCBI C++ toolkit. The source code\ for the entire toolkit is available from the NCBI\ \ FTP site.\
\ \\ To create this track, WindowMasker was run with the following parameters:\
\ windowmasker -mk_counts true -input ce11.fa -output wm_counts\ windowmasker -ustat wm_counts -sdust true -input ce11.fa -output repeats.bed\\ The repeats.bed (BED3) file was loaded into the "windowmaskerSdust" table for\ this track.\ \ \
\ Morgulis A, Gertz EM, Schäffer AA, Agarwala R.\ WindowMasker: window-based masker for sequenced genomes.\ Bioinformatics. 2006 Jan 15;22(2):134-41.\ PMID: 16287941\
\ varRep 1 group varRep\ longLabel Genomic Intervals Masked by WindowMasker + SDust\ shortLabel WM + SDust\ track windowmaskerSdust\ type bed 3\ visibility hide\ chainPanRed1 panRed1 Chain chain panRed1 Microworm (Feb. 2013 (WS240/Pred3/panRed1)) Chained Alignments 3 101 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Microworm (Feb. 2013 (WS240/Pred3/panRed1)) Chained Alignments\ otherDb panRed1\ parent nematodesChainNetViewchain off\ shortLabel panRed1 Chain\ subGroups view=chain species=s083 clade=c02\ track chainPanRed1\ type chain panRed1\ netPanRed1 panRed1 Net netAlign panRed1 chainPanRed1 Microworm (Feb. 2013 (WS240/Pred3/panRed1)) Alignment Net 1 102 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Microworm (Feb. 2013 (WS240/Pred3/panRed1)) Alignment Net\ otherDb panRed1\ parent nematodesChainNetViewnet off\ shortLabel panRed1 Net\ subGroups view=net species=s083 clade=c02\ track netPanRed1\ type netAlign panRed1 chainPanRed1\ chainBurXyl1 burXyl1 Chain chain burXyl1 Pine wood nematode (Nov. 2011 (WS229/B. xylophilus Ka4C1/burXyl1)) Chained Alignments 3 103 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Pine wood nematode (Nov. 2011 (WS229/B. xylophilus Ka4C1/burXyl1)) Chained Alignments\ otherDb burXyl1\ parent nematodesChainNetViewchain off\ shortLabel burXyl1 Chain\ subGroups view=chain species=s084 clade=c02\ track chainBurXyl1\ type chain burXyl1\ netBurXyl1 burXyl1 Net netAlign burXyl1 chainBurXyl1 Pine wood nematode (Nov. 2011 (WS229/B. xylophilus Ka4C1/burXyl1)) Alignment Net 1 104 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Pine wood nematode (Nov. 2011 (WS229/B. xylophilus Ka4C1/burXyl1)) Alignment Net\ otherDb burXyl1\ parent nematodesChainNetViewnet off\ shortLabel burXyl1 Net\ subGroups view=net species=s084 clade=c02\ track netBurXyl1\ type netAlign burXyl1 chainBurXyl1\ chainMelHap1 melHap1 Chain chain melHap1 M. hapla (Sep. 2008 (M. hapla VW9 WS210/melHap1)) Chained Alignments 3 105 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel M. hapla (Sep. 2008 (M. hapla VW9 WS210/melHap1)) Chained Alignments\ otherDb melHap1\ parent nematodesChainNetViewchain off\ shortLabel melHap1 Chain\ subGroups view=chain species=s085 clade=c02\ track chainMelHap1\ type chain melHap1\ netMelHap1 melHap1 Net netAlign melHap1 chainMelHap1 M. hapla (Sep. 2008 (M. hapla VW9 WS210/melHap1)) Alignment Net 1 106 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel M. hapla (Sep. 2008 (M. hapla VW9 WS210/melHap1)) Alignment Net\ otherDb melHap1\ parent nematodesChainNetViewnet off\ shortLabel melHap1 Net\ subGroups view=net species=s085 clade=c02\ track netMelHap1\ type netAlign melHap1 chainMelHap1\ chainMelInc2 melInc2 Chain chain melInc2 M. incognita (Feb. 2008 (M. incognita WS245/PRJEA28837/melInc2)) Chained Alignments 3 107 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel M. incognita (Feb. 2008 (M. incognita WS245/PRJEA28837/melInc2)) Chained Alignments\ otherDb melInc2\ parent nematodesChainNetViewchain off\ shortLabel melInc2 Chain\ subGroups view=chain species=s086 clade=c02\ track chainMelInc2\ type chain melInc2\ netMelInc2 melInc2 Net netAlign melInc2 chainMelInc2 M. incognita (Feb. 2008 (M. incognita WS245/PRJEA28837/melInc2)) Alignment Net 1 108 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel M. incognita (Feb. 2008 (M. incognita WS245/PRJEA28837/melInc2)) Alignment Net\ otherDb melInc2\ parent nematodesChainNetViewnet off\ shortLabel melInc2 Net\ subGroups view=net species=s086 clade=c02\ track netMelInc2\ type netAlign melInc2 chainMelInc2\ chainDictyocaulus_viviparus Dictyocaulus_viviparus Chain chain Dictyocaulus_viviparus Dictyocaulus_viviparus (Dictyocaulus_viviparus) Chained Alignments 3 109 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Dictyocaulus_viviparus (Dictyocaulus_viviparus) Chained Alignments\ otherDb Dictyocaulus_viviparus\ parent nematodesChainNetViewchain off\ shortLabel Dictyocaulus_viviparus Chain\ subGroups view=chain species=s087 clade=c03\ track chainDictyocaulus_viviparus\ type chain Dictyocaulus_viviparus\ chainNippostrongylus_brasiliensis Nippostrongylus_brasiliensis Chain chain Nippostrongylus_brasiliensis Nippostrongylus_brasiliensis (Nippostrongylus_brasiliensis) Chained Alignments 3 110 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Nippostrongylus_brasiliensis (Nippostrongylus_brasiliensis) Chained Alignments\ otherDb Nippostrongylus_brasiliensis\ parent nematodesChainNetViewchain off\ shortLabel Nippostrongylus_brasiliensis Chain\ subGroups view=chain species=s088 clade=c03\ track chainNippostrongylus_brasiliensis\ type chain Nippostrongylus_brasiliensis\ chainHeligmosomoides_polygyrus_bakeri Heligmosomoides_polygyrus_bakeri Chain chain Heligmosomoides_polygyrus_bakeri Heligmosomoides_polygyrus_bakeri (Heligmosomoides_polygyrus_bakeri) Chained Alignments 3 111 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Heligmosomoides_polygyrus_bakeri (Heligmosomoides_polygyrus_bakeri) Chained Alignments\ otherDb Heligmosomoides_polygyrus_bakeri\ parent nematodesChainNetViewchain off\ shortLabel Heligmosomoides_polygyrus_bakeri Chain\ subGroups view=chain species=s089 clade=c03\ track chainHeligmosomoides_polygyrus_bakeri\ type chain Heligmosomoides_polygyrus_bakeri\ chainTeladorsagia_circumcincta Teladorsagia_circumcincta Chain chain Teladorsagia_circumcincta Teladorsagia_circumcincta (Teladorsagia_circumcincta) Chained Alignments 3 112 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Teladorsagia_circumcincta (Teladorsagia_circumcincta) Chained Alignments\ otherDb Teladorsagia_circumcincta\ parent nematodesChainNetViewchain off\ shortLabel Teladorsagia_circumcincta Chain\ subGroups view=chain species=s090 clade=c03\ track chainTeladorsagia_circumcincta\ type chain Teladorsagia_circumcincta\ chainHaemonchus_contortus Haemonchus_contortus Chain chain Haemonchus_contortus Haemonchus_contortus (Haemonchus_contortus) Chained Alignments 3 113 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Haemonchus_contortus (Haemonchus_contortus) Chained Alignments\ otherDb Haemonchus_contortus\ parent nematodesChainNetViewchain off\ shortLabel Haemonchus_contortus Chain\ subGroups view=chain species=s091 clade=c03\ track chainHaemonchus_contortus\ type chain Haemonchus_contortus\ chainAngiostrongylus_cantonensis Angiostrongylus_cantonensis Chain chain Angiostrongylus_cantonensis Angiostrongylus_cantonensis (Angiostrongylus_cantonensis) Chained Alignments 3 114 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Angiostrongylus_cantonensis (Angiostrongylus_cantonensis) Chained Alignments\ otherDb Angiostrongylus_cantonensis\ parent nematodesChainNetViewchain off\ shortLabel Angiostrongylus_cantonensis Chain\ subGroups view=chain species=s092 clade=c03\ track chainAngiostrongylus_cantonensis\ type chain Angiostrongylus_cantonensis\ chainHaeCon2 haeCon2 Chain chain haeCon2 Barber pole worm (Jul. 2013 (WormBase WS239/haeCon2)) Chained Alignments 3 115 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Barber pole worm (Jul. 2013 (WormBase WS239/haeCon2)) Chained Alignments\ otherDb haeCon2\ parent nematodesChainNetViewchain off\ shortLabel haeCon2 Chain\ subGroups view=chain species=s093 clade=c03\ track chainHaeCon2\ type chain haeCon2\ netHaeCon2 haeCon2 Net netAlign haeCon2 chainHaeCon2 Barber pole worm (Jul. 2013 (WormBase WS239/haeCon2)) Alignment Net 1 116 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Barber pole worm (Jul. 2013 (WormBase WS239/haeCon2)) Alignment Net\ otherDb haeCon2\ parent nematodesChainNetViewnet off\ shortLabel haeCon2 Net\ subGroups view=net species=s093 clade=c03\ track netHaeCon2\ type netAlign haeCon2 chainHaeCon2\ chainPlectus_sambesii Plectus_sambesii Chain chain Plectus_sambesii Plectus_sambesii (Plectus_sambesii) Chained Alignments 3 117 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Plectus_sambesii (Plectus_sambesii) Chained Alignments\ otherDb Plectus_sambesii\ parent nematodesChainNetViewchain off\ shortLabel Plectus_sambesii Chain\ subGroups view=chain species=s094 clade=c04\ track chainPlectus_sambesii\ type chain Plectus_sambesii\ chainTrichinella_murrelli Trichinella_murrelli Chain chain Trichinella_murrelli Trichinella_murrelli (Trichinella_murrelli) Chained Alignments 3 118 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Trichinella_murrelli (Trichinella_murrelli) Chained Alignments\ otherDb Trichinella_murrelli\ parent nematodesChainNetViewchain off\ shortLabel Trichinella_murrelli Chain\ subGroups view=chain species=s095 clade=c05\ track chainTrichinella_murrelli\ type chain Trichinella_murrelli\ chainTrichinella_zimbabwensis Trichinella_zimbabwensis Chain chain Trichinella_zimbabwensis Trichinella_zimbabwensis (Trichinella_zimbabwensis) Chained Alignments 3 119 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Trichinella_zimbabwensis (Trichinella_zimbabwensis) Chained Alignments\ otherDb Trichinella_zimbabwensis\ parent nematodesChainNetViewchain off\ shortLabel Trichinella_zimbabwensis Chain\ subGroups view=chain species=s096 clade=c05\ track chainTrichinella_zimbabwensis\ type chain Trichinella_zimbabwensis\ chainTrichinella_pseudospiralis Trichinella_pseudospiralis Chain chain Trichinella_pseudospiralis Trichinella_pseudospiralis (Trichinella_pseudospiralis) Chained Alignments 3 120 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Trichinella_pseudospiralis (Trichinella_pseudospiralis) Chained Alignments\ otherDb Trichinella_pseudospiralis\ parent nematodesChainNetViewchain off\ shortLabel Trichinella_pseudospiralis Chain\ subGroups view=chain species=s097 clade=c05\ track chainTrichinella_pseudospiralis\ type chain Trichinella_pseudospiralis\ chainTrichinella_papuae Trichinella_papuae Chain chain Trichinella_papuae Trichinella_papuae (Trichinella_papuae) Chained Alignments 3 121 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Trichinella_papuae (Trichinella_papuae) Chained Alignments\ otherDb Trichinella_papuae\ parent nematodesChainNetViewchain off\ shortLabel Trichinella_papuae Chain\ subGroups view=chain species=s098 clade=c05\ track chainTrichinella_papuae\ type chain Trichinella_papuae\ chainTrichinella_T6 Trichinella_T6 Chain chain Trichinella_T6 Trichinella_T6 (Trichinella_T6) Chained Alignments 3 122 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Trichinella_T6 (Trichinella_T6) Chained Alignments\ otherDb Trichinella_T6\ parent nematodesChainNetViewchain off\ shortLabel Trichinella_T6 Chain\ subGroups view=chain species=s099 clade=c05\ track chainTrichinella_T6\ type chain Trichinella_T6\ chainTrichinella_britovi Trichinella_britovi Chain chain Trichinella_britovi Trichinella_britovi (Trichinella_britovi) Chained Alignments 3 123 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Trichinella_britovi (Trichinella_britovi) Chained Alignments\ otherDb Trichinella_britovi\ parent nematodesChainNetViewchain off\ shortLabel Trichinella_britovi Chain\ subGroups view=chain species=s100 clade=c05\ track chainTrichinella_britovi\ type chain Trichinella_britovi\ chainTrichinella_T8 Trichinella_T8 Chain chain Trichinella_T8 Trichinella_T8 (Trichinella_T8) Chained Alignments 3 124 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Trichinella_T8 (Trichinella_T8) Chained Alignments\ otherDb Trichinella_T8\ parent nematodesChainNetViewchain off\ shortLabel Trichinella_T8 Chain\ subGroups view=chain species=s101 clade=c05\ track chainTrichinella_T8\ type chain Trichinella_T8\ chainTrichinella_T9 Trichinella_T9 Chain chain Trichinella_T9 Trichinella_T9 (Trichinella_T9) Chained Alignments 3 125 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Trichinella_T9 (Trichinella_T9) Chained Alignments\ otherDb Trichinella_T9\ parent nematodesChainNetViewchain off\ shortLabel Trichinella_T9 Chain\ subGroups view=chain species=s102 clade=c05\ track chainTrichinella_T9\ type chain Trichinella_T9\ chainTrichinella_patagoniensis Trichinella_patagoniensis Chain chain Trichinella_patagoniensis Trichinella_patagoniensis (Trichinella_patagoniensis) Chained Alignments 3 126 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Trichinella_patagoniensis (Trichinella_patagoniensis) Chained Alignments\ otherDb Trichinella_patagoniensis\ parent nematodesChainNetViewchain off\ shortLabel Trichinella_patagoniensis Chain\ subGroups view=chain species=s103 clade=c05\ track chainTrichinella_patagoniensis\ type chain Trichinella_patagoniensis\ chainTrichinella_nelsoni Trichinella_nelsoni Chain chain Trichinella_nelsoni Trichinella_nelsoni (Trichinella_nelsoni) Chained Alignments 3 127 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Trichinella_nelsoni (Trichinella_nelsoni) Chained Alignments\ otherDb Trichinella_nelsoni\ parent nematodesChainNetViewchain off\ shortLabel Trichinella_nelsoni Chain\ subGroups view=chain species=s104 clade=c05\ track chainTrichinella_nelsoni\ type chain Trichinella_nelsoni\ chainTrichinella_nativa Trichinella_nativa Chain chain Trichinella_nativa Trichinella_nativa (Trichinella_nativa) Chained Alignments 3 128 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Trichinella_nativa (Trichinella_nativa) Chained Alignments\ otherDb Trichinella_nativa\ parent nematodesChainNetViewchain off\ shortLabel Trichinella_nativa Chain\ subGroups view=chain species=s105 clade=c05\ track chainTrichinella_nativa\ type chain Trichinella_nativa\ chainTrichinella_spiralis Trichinella_spiralis Chain chain Trichinella_spiralis Trichinella_spiralis (Trichinella_spiralis) Chained Alignments 3 129 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Trichinella_spiralis (Trichinella_spiralis) Chained Alignments\ otherDb Trichinella_spiralis\ parent nematodesChainNetViewchain off\ shortLabel Trichinella_spiralis Chain\ subGroups view=chain species=s106 clade=c05\ track chainTrichinella_spiralis\ type chain Trichinella_spiralis\ chainRomanomermis_culicivorax Romanomermis_culicivorax Chain chain Romanomermis_culicivorax Romanomermis_culicivorax (Romanomermis_culicivorax) Chained Alignments 3 130 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Romanomermis_culicivorax (Romanomermis_culicivorax) Chained Alignments\ otherDb Romanomermis_culicivorax\ parent nematodesChainNetViewchain off\ shortLabel Romanomermis_culicivorax Chain\ subGroups view=chain species=s107 clade=c05\ track chainRomanomermis_culicivorax\ type chain Romanomermis_culicivorax\ chainTrichuris_trichiura Trichuris_trichiura Chain chain Trichuris_trichiura Trichuris_trichiura (Trichuris_trichiura) Chained Alignments 3 131 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Trichuris_trichiura (Trichuris_trichiura) Chained Alignments\ otherDb Trichuris_trichiura\ parent nematodesChainNetViewchain off\ shortLabel Trichuris_trichiura Chain\ subGroups view=chain species=s108 clade=c05\ track chainTrichuris_trichiura\ type chain Trichuris_trichiura\ chainTrichuris_muris Trichuris_muris Chain chain Trichuris_muris Trichuris_muris (Trichuris_muris) Chained Alignments 3 132 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Trichuris_muris (Trichuris_muris) Chained Alignments\ otherDb Trichuris_muris\ parent nematodesChainNetViewchain off\ shortLabel Trichuris_muris Chain\ subGroups view=chain species=s109 clade=c05\ track chainTrichuris_muris\ type chain Trichuris_muris\ chainTriSui1 triSui1 Chain chain triSui1 Whipworm (Jul. 2014 (WS243/T. suis DCEP-RM93M male/triSui1)) Chained Alignments 3 133 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Whipworm (Jul. 2014 (WS243/T. suis DCEP-RM93M male/triSui1)) Chained Alignments\ otherDb triSui1\ parent nematodesChainNetViewchain off\ shortLabel triSui1 Chain\ subGroups view=chain species=s110 clade=c05\ track chainTriSui1\ type chain triSui1\ netTriSui1 triSui1 Net netAlign triSui1 chainTriSui1 Whipworm (Jul. 2014 (WS243/T. suis DCEP-RM93M male/triSui1)) Alignment Net 1 134 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Whipworm (Jul. 2014 (WS243/T. suis DCEP-RM93M male/triSui1)) Alignment Net\ otherDb triSui1\ parent nematodesChainNetViewnet off\ shortLabel triSui1 Net\ subGroups view=net species=s110 clade=c05\ track netTriSui1\ type netAlign triSui1 chainTriSui1\ chainTriSpi1 triSpi1 Chain chain triSpi1 Trichinella (Jan. 2011 (WS225/Trichinella_spiralis-3.7.1/triSpi1)) Chained Alignments 3 135 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Trichinella (Jan. 2011 (WS225/Trichinella_spiralis-3.7.1/triSpi1)) Chained Alignments\ otherDb triSpi1\ parent nematodesChainNetViewchain off\ shortLabel triSpi1 Chain\ subGroups view=chain species=s111 clade=c05\ track chainTriSpi1\ type chain triSpi1\ netTriSpi1 triSpi1 Net netAlign triSpi1 chainTriSpi1 Trichinella (Jan. 2011 (WS225/Trichinella_spiralis-3.7.1/triSpi1)) Alignment Net 1 136 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel Trichinella (Jan. 2011 (WS225/Trichinella_spiralis-3.7.1/triSpi1)) Alignment Net\ otherDb triSpi1\ parent nematodesChainNetViewnet off\ shortLabel triSpi1 Net\ subGroups view=net species=s111 clade=c05\ track netTriSpi1\ type netAlign triSpi1 chainTriSpi1\ chainSchmidtea_mediterranea Schmidtea_mediterranea Chain chain Schmidtea_mediterranea Schmidtea_mediterranea (Schmidtea_mediterranea) Chained Alignments 3 137 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Schmidtea_mediterranea (Schmidtea_mediterranea) Chained Alignments\ otherDb Schmidtea_mediterranea\ parent nematodesChainNetViewchain off\ shortLabel Schmidtea_mediterranea Chain\ subGroups view=chain species=s112 clade=c06\ track chainSchmidtea_mediterranea\ type chain Schmidtea_mediterranea\ chainGirardia_tigrina Girardia_tigrina Chain chain Girardia_tigrina Girardia_tigrina (Girardia_tigrina) Chained Alignments 3 138 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Girardia_tigrina (Girardia_tigrina) Chained Alignments\ otherDb Girardia_tigrina\ parent nematodesChainNetViewchain off\ shortLabel Girardia_tigrina Chain\ subGroups view=chain species=s113 clade=c06\ track chainGirardia_tigrina\ type chain Girardia_tigrina\ chainDugesia_japonica Dugesia_japonica Chain chain Dugesia_japonica Dugesia_japonica (Dugesia_japonica) Chained Alignments 3 139 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Dugesia_japonica (Dugesia_japonica) Chained Alignments\ otherDb Dugesia_japonica\ parent nematodesChainNetViewchain off\ shortLabel Dugesia_japonica Chain\ subGroups view=chain species=s114 clade=c06\ track chainDugesia_japonica\ type chain Dugesia_japonica\ chainMacrostomum_lignano Macrostomum_lignano Chain chain Macrostomum_lignano Macrostomum_lignano (Macrostomum_lignano) Chained Alignments 3 140 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Macrostomum_lignano (Macrostomum_lignano) Chained Alignments\ otherDb Macrostomum_lignano\ parent nematodesChainNetViewchain off\ shortLabel Macrostomum_lignano Chain\ subGroups view=chain species=s115 clade=c06\ track chainMacrostomum_lignano\ type chain Macrostomum_lignano\ chainSchistosoma_mansoni Schistosoma_mansoni Chain chain Schistosoma_mansoni Schistosoma_mansoni (Schistosoma_mansoni) Chained Alignments 3 141 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Schistosoma_mansoni (Schistosoma_mansoni) Chained Alignments\ otherDb Schistosoma_mansoni\ parent nematodesChainNetViewchain off\ shortLabel Schistosoma_mansoni Chain\ subGroups view=chain species=s116 clade=c06\ track chainSchistosoma_mansoni\ type chain Schistosoma_mansoni\ chainSchistosoma_haematobium Schistosoma_haematobium Chain chain Schistosoma_haematobium Schistosoma_haematobium (Schistosoma_haematobium) Chained Alignments 3 142 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Schistosoma_haematobium (Schistosoma_haematobium) Chained Alignments\ otherDb Schistosoma_haematobium\ parent nematodesChainNetViewchain off\ shortLabel Schistosoma_haematobium Chain\ subGroups view=chain species=s117 clade=c06\ track chainSchistosoma_haematobium\ type chain Schistosoma_haematobium\ chainSchistosoma_japonicum Schistosoma_japonicum Chain chain Schistosoma_japonicum Schistosoma_japonicum (Schistosoma_japonicum) Chained Alignments 3 143 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Schistosoma_japonicum (Schistosoma_japonicum) Chained Alignments\ otherDb Schistosoma_japonicum\ parent nematodesChainNetViewchain off\ shortLabel Schistosoma_japonicum Chain\ subGroups view=chain species=s118 clade=c06\ track chainSchistosoma_japonicum\ type chain Schistosoma_japonicum\ chainGyrodactylus_salaris Gyrodactylus_salaris Chain chain Gyrodactylus_salaris Gyrodactylus_salaris (Gyrodactylus_salaris) Chained Alignments 3 144 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Gyrodactylus_salaris (Gyrodactylus_salaris) Chained Alignments\ otherDb Gyrodactylus_salaris\ parent nematodesChainNetViewchain off\ shortLabel Gyrodactylus_salaris Chain\ subGroups view=chain species=s119 clade=c06\ track chainGyrodactylus_salaris\ type chain Gyrodactylus_salaris\ chainHymenolepis_microstoma Hymenolepis_microstoma Chain chain Hymenolepis_microstoma Hymenolepis_microstoma (Hymenolepis_microstoma) Chained Alignments 3 145 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Hymenolepis_microstoma (Hymenolepis_microstoma) Chained Alignments\ otherDb Hymenolepis_microstoma\ parent nematodesChainNetViewchain off\ shortLabel Hymenolepis_microstoma Chain\ subGroups view=chain species=s120 clade=c06\ track chainHymenolepis_microstoma\ type chain Hymenolepis_microstoma\ chainFasciola_hepatica Fasciola_hepatica Chain chain Fasciola_hepatica Fasciola_hepatica (Fasciola_hepatica) Chained Alignments 3 146 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Fasciola_hepatica (Fasciola_hepatica) Chained Alignments\ otherDb Fasciola_hepatica\ parent nematodesChainNetViewchain off\ shortLabel Fasciola_hepatica Chain\ subGroups view=chain species=s121 clade=c06\ track chainFasciola_hepatica\ type chain Fasciola_hepatica\ chainTaenia_multiceps Taenia_multiceps Chain chain Taenia_multiceps Taenia_multiceps (Taenia_multiceps) Chained Alignments 3 147 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Taenia_multiceps (Taenia_multiceps) Chained Alignments\ otherDb Taenia_multiceps\ parent nematodesChainNetViewchain off\ shortLabel Taenia_multiceps Chain\ subGroups view=chain species=s122 clade=c06\ track chainTaenia_multiceps\ type chain Taenia_multiceps\ chainFasciola_gigantica Fasciola_gigantica Chain chain Fasciola_gigantica Fasciola_gigantica (Fasciola_gigantica) Chained Alignments 3 148 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Fasciola_gigantica (Fasciola_gigantica) Chained Alignments\ otherDb Fasciola_gigantica\ parent nematodesChainNetViewchain off\ shortLabel Fasciola_gigantica Chain\ subGroups view=chain species=s123 clade=c06\ track chainFasciola_gigantica\ type chain Fasciola_gigantica\ chainTaenia_saginata Taenia_saginata Chain chain Taenia_saginata Taenia_saginata (Taenia_saginata) Chained Alignments 3 149 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Taenia_saginata (Taenia_saginata) Chained Alignments\ otherDb Taenia_saginata\ parent nematodesChainNetViewchain off\ shortLabel Taenia_saginata Chain\ subGroups view=chain species=s124 clade=c06\ track chainTaenia_saginata\ type chain Taenia_saginata\ rmsk RepeatMasker rmsk Repeating Elements by RepeatMasker 0 149.1 0 0 0 127 127 127 1 0 0\
This track was created by using Arian Smit's
\ In full display mode, this track displays up to ten different classes of repeats:\
\ The level of color shading in the graphical display reflects the amount of \ base mismatch, base deletion, and base insertion associated with a repeat \ element. The higher the combined number of these, the lighter the shading.
\ \\ UCSC has used the most current versions of the RepeatMasker software \ and repeat libraries available to generate these data. Note that these \ versions may be newer than those that are publicly available on the Internet. \
\\ Data are generated using the RepeatMasker -s flag. Additional flags\ may be used for certain organisms. Repeats are soft-masked. Alignments may \ extend through repeats, but are not permitted to initiate in them. \ See the \ FAQ for \ more information.
\ \\ Thanks to Arian Smit, Robert Hubley and GIRI\ for providing the tools and repeat libraries used to generate this track.
\ \\ Repbase Update is described in\ Jurka J.\ Repbase update: a database and an electronic journal of repetitive elements.\ Trends Genet. 2000 Sep;16(9):418-420.
\ varRep 0 canPack off\ group varRep\ longLabel Repeating Elements by RepeatMasker\ priority 149.1\ shortLabel RepeatMasker\ spectrum on\ track rmsk\ type rmsk\ visibility hide\ chainClonorchis_sinensis Clonorchis_sinensis Chain chain Clonorchis_sinensis Clonorchis_sinensis (Clonorchis_sinensis) Chained Alignments 3 150 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Clonorchis_sinensis (Clonorchis_sinensis) Chained Alignments\ otherDb Clonorchis_sinensis\ parent nematodesChainNetViewchain off\ shortLabel Clonorchis_sinensis Chain\ subGroups view=chain species=s125 clade=c06\ track chainClonorchis_sinensis\ type chain Clonorchis_sinensis\ chainOpisthorchis_viverrini Opisthorchis_viverrini Chain chain Opisthorchis_viverrini Opisthorchis_viverrini (Opisthorchis_viverrini) Chained Alignments 3 151 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Opisthorchis_viverrini (Opisthorchis_viverrini) Chained Alignments\ otherDb Opisthorchis_viverrini\ parent nematodesChainNetViewchain off\ shortLabel Opisthorchis_viverrini Chain\ subGroups view=chain species=s126 clade=c06\ track chainOpisthorchis_viverrini\ type chain Opisthorchis_viverrini\ chainEchinococcus_multilocularis Echinococcus_multilocularis Chain chain Echinococcus_multilocularis Echinococcus_multilocularis (Echinococcus_multilocularis) Chained Alignments 3 152 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Echinococcus_multilocularis (Echinococcus_multilocularis) Chained Alignments\ otherDb Echinococcus_multilocularis\ parent nematodesChainNetViewchain off\ shortLabel Echinococcus_multilocularis Chain\ subGroups view=chain species=s127 clade=c06\ track chainEchinococcus_multilocularis\ type chain Echinococcus_multilocularis\ chainTaenia_asiatica Taenia_asiatica Chain chain Taenia_asiatica Taenia_asiatica (Taenia_asiatica) Chained Alignments 3 153 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Taenia_asiatica (Taenia_asiatica) Chained Alignments\ otherDb Taenia_asiatica\ parent nematodesChainNetViewchain off\ shortLabel Taenia_asiatica Chain\ subGroups view=chain species=s128 clade=c06\ track chainTaenia_asiatica\ type chain Taenia_asiatica\ chainEchinococcus_canadensis Echinococcus_canadensis Chain chain Echinococcus_canadensis Echinococcus_canadensis (Echinococcus_canadensis) Chained Alignments 3 154 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Echinococcus_canadensis (Echinococcus_canadensis) Chained Alignments\ otherDb Echinococcus_canadensis\ parent nematodesChainNetViewchain off\ shortLabel Echinococcus_canadensis Chain\ subGroups view=chain species=s129 clade=c06\ track chainEchinococcus_canadensis\ type chain Echinococcus_canadensis\ chainTaenia_solium Taenia_solium Chain chain Taenia_solium Taenia_solium (Taenia_solium) Chained Alignments 3 155 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Taenia_solium (Taenia_solium) Chained Alignments\ otherDb Taenia_solium\ parent nematodesChainNetViewchain off\ shortLabel Taenia_solium Chain\ subGroups view=chain species=s130 clade=c06\ track chainTaenia_solium\ type chain Taenia_solium\ chainEchinococcus_granulosus Echinococcus_granulosus Chain chain Echinococcus_granulosus Echinococcus_granulosus (Echinococcus_granulosus) Chained Alignments 3 156 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Echinococcus_granulosus (Echinococcus_granulosus) Chained Alignments\ otherDb Echinococcus_granulosus\ parent nematodesChainNetViewchain off\ shortLabel Echinococcus_granulosus Chain\ subGroups view=chain species=s131 clade=c06\ track chainEchinococcus_granulosus\ type chain Echinococcus_granulosus\ chainSpirometra_erinaceieuropaei Spirometra_erinaceieuropaei Chain chain Spirometra_erinaceieuropaei Spirometra_erinaceieuropaei (Spirometra_erinaceieuropaei) Chained Alignments 3 157 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Spirometra_erinaceieuropaei (Spirometra_erinaceieuropaei) Chained Alignments\ otherDb Spirometra_erinaceieuropaei\ parent nematodesChainNetViewchain off\ shortLabel Spirometra_erinaceieuropaei Chain\ subGroups view=chain species=s132 clade=c06\ track chainSpirometra_erinaceieuropaei\ type chain Spirometra_erinaceieuropaei\ chainDicrocoelium_dendriticum Dicrocoelium_dendriticum Chain chain Dicrocoelium_dendriticum Dicrocoelium_dendriticum (Dicrocoelium_dendriticum) Chained Alignments 3 158 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel Dicrocoelium_dendriticum (Dicrocoelium_dendriticum) Chained Alignments\ otherDb Dicrocoelium_dendriticum\ parent nematodesChainNetViewchain off\ shortLabel Dicrocoelium_dendriticum Chain\ subGroups view=chain species=s133 clade=c06\ track chainDicrocoelium_dendriticum\ type chain Dicrocoelium_dendriticum\ chainCi3 C. intestinalis Chain chain ci3 C. intestinalis (Apr. 2011 (Kyoto KH/ci3)) Chained Alignments 3 159 0 0 0 255 255 0 1 0 0 compGeno 1 longLabel C. intestinalis (Apr. 2011 (Kyoto KH/ci3)) Chained Alignments\ otherDb ci3\ parent nematodesChainNetViewchain off\ shortLabel C. intestinalis Chain\ subGroups view=chain species=s134 clade=c07\ track chainCi3\ type chain ci3\ netCi3 C. intestinalis Net netAlign ci3 chainCi3 C. intestinalis (Apr. 2011 (Kyoto KH/ci3)) Alignment Net 1 160 0 0 0 255 255 0 0 0 0 compGeno 0 longLabel C. intestinalis (Apr. 2011 (Kyoto KH/ci3)) Alignment Net\ otherDb ci3\ parent nematodesChainNetViewnet off\ shortLabel C. intestinalis Net\ subGroups view=net species=s134 clade=c07\ track netCi3\ type netAlign ci3 chainCi3\ chainSelf Self Chain chain ce11 C. elegans Chained Self Alignments 0 400 100 50 0 255 240 200 1 0 0\ This track shows alignments of the C. elegans genome with itself, \ using a gap scoring system that allows longer gaps than traditional\ affine gap scoring systems. The system can also tolerate gaps\ in both sets of sequence simultaneously. After filtering out the \ "trivial" alignments produced when identical locations of the \ genome map to one another (e.g. chrN mapping to chrN), \ the remaining alignments point out areas of duplication within the \ C. elegans genome.
\\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions. Single lines indicate \ gaps that are largely due to a deletion in the query assembly or an \ insertion in the target assembly. Double lines represent more complex gaps \ that involve substantial sequence in both the query and target assemblies. \ This may result from inversions, overlapping deletions, an abundance of local \ mutation, or an unsequenced gap in one of the assemblies. In cases where \ multiple chains align over a particular region of the C. elegans \ genome, the chains with single-lined gaps are often due to processed \ pseudogenes, while chains with double-lined gaps are more often due to \ paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \ \By default, the chains to chromosome-based assemblies are colored\ based on which chromosome they map to in the aligning organism. To turn\ off the coloring, check the "off" button next to: Color\ track based on chromosome.
\\ To display only the chains of one chromosome in the aligning\ organism, enter the name of that chromosome (e.g. chr4) in box next to: \ Filter by chromosome.
\ \\ The genome was aligned to itself using blastz. Trivial alignments were \ filtered out, and the remaining alignments were converted into axt format\ using the lavToAxt program. The axt alignments were fed into axtChain, which \ organizes all alignments between a single target chromosome and a single\ query chromosome into a group and creates a kd-tree out of the gapless \ subsections (blocks) of the alignments. A dynamic program was then run over \ the kd-trees to find the maximally scoring chains of these blocks. Chains \ scoring below a threshold were discarded; the remaining chains are displayed \ in this track.
\ \\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his\ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California\ at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.\
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte F, Yap VB, Miller W.\ Scoring pairwise genomic sequence alignments.\ Pac Symp Biocomput. 2002:115-26.\ PMID: 11928468\
\ \\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
Evolution's cauldron: Duplication, deletion, and rearrangement\
in the mouse and human genomes.\
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.\
PMID: 14500911; PMC:
\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R,\
Haussler D, Miller W.\
Human-Mouse Alignments with BLASTZ.\
Genome Res. 2003 Jan;13(1):103-7.\
PMID: 12529312; PMC: