\ This track shows the draft assembly of the C. brenneri genome. \ \ The assembly is 9.5X WGS coverage. The 10,292 supercontigs are displayed\ in the UCSC Genome browser as a single artifical chromosome chrUn with an\ artifical gap of 1,000 N's between supercontigs. The largest supercontig\ is 1,129,006, with 478 supercontigs larger than 93,185 bp (N50) containing\ over %50 of the sequence.\ \
\ In dense mode, this track depicts the supercontigs. Supercontig boundaries\ are distinguished by the use of alternating gold and brown \ coloration. Arbitrary 1000 base gaps exist between the supercontigs, shown as\ spaces between the gold and brown blocks.\
\\ All components within this track are of fragment type "W": \ Whole Genome Shotgun contig.
\ \\ The Jan. 2007 Caenorhabditis brenneri\ (aka: Caenorhabditis n. sp. 4. PB2801) draft assembly\ produced by\ \ Washington University School of Medicine GSC with the following\ data usage policy.\
\\ As described at WormBase: "This is a 20X inbred (one gravid female per\ generation) derivative of LKC28, which is conspecific with CB5161."\ Recently renamed to C. brenneri. Other conspecific\ strains: SB129, SB280. See also:\ Zootaxa 1456: 45-62 (25 Apr. 2007),\ \ Walter Sudhaus and Karin Kiontke.\
\ map 1 altColor 230,170,40\ color 150,100,30\ group map\ longLabel Assembly Scaffolds (Supercontigs)\ priority 9\ shortLabel Scaffolds\ track gold\ type bed 3 +\ visibility hide\ ctgPos2 Contigs ctgPos Assembly Contigs 0 10 0 0 0 127 127 127 0 0 0\ This track shows the contigs used to assemble the supercontigs\ in the draft assembly of the C. brenneri genome. \
\\ The assembly is 9.5X WGS coverage. The 10,292 supercontigs are displayed\ in the UCSC Genome browser as a single artifical chromosome chrUn with an\ artifical gap of 1,000 N's between supercontigs. The largest supercontig\ is 1,129,006, with 478 supercontigs larger than 93,185 bp (N50) containing\ over %50 of the sequence.\
\\ The Jan. 2007 Caenorhabditis brenneri\ (aka: Caenorhabditis n. sp. 4. PB2801) draft assembly\ produced by\ \ Washington University School of Medicine GSC with the following\ data usage policy.\
\\ As described at WormBase: "This is a 20X inbred (one gravid female per\ generation) derivative of LKC28, which is conspecific with CB5161."\ Recently renamed to C. brenneri. Other conspecific\ strains: SB129, SB280. See also:\ Zootaxa 1456: 45-62 (25 Apr. 2007),\ \ Walter Sudhaus and Karin Kiontke.\
\ map 0 group map\ longLabel Assembly Contigs\ priority 10\ shortLabel Contigs\ track ctgPos2\ type ctgPos\ visibility hide\ mrna C. brenneri mRNAs psl . C. brenneri mRNAs from GenBank 3 100 0 0 0 127 127 127 1 0 0\ The mRNA track shows alignments between C. brenneri 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. brenneri 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 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\ gap Gap bed 3 + Gap Locations 1 100 0 0 0 127 127 127 0 0 0\ 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 two types of gaps:\
\ The Jan. 2007 Caenorhabditis brenneri\ (aka: Caenorhabditis n. sp. 4. PB2801) draft assembly\ produced by\ \ Washington University School of Medicine GSC with the following\ data usage policy.\
\\ As described at WormBase: "This is a 20X inbred (one gravid female per generation) derivative of LKC28, which is conspecific with CB5161." Recently renamed\ to C. brenneri. Other conspecific strains: SB129, SB280. See also:\ Zootaxa 1456: 45-62 (25 Apr. 2007),\ \ Walter Sudhaus and Karin Kiontke.\
\ map 1 group map\ longLabel Gap Locations\ shortLabel Gap\ track gap\ type bed 3 +\ visibility dense\ gc5Base GC Percent wig 0 100 GC Percent in 5-Base Windows 0 100 0 0 0 128 128 128 0 0 0\ 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\ longLabel GC Percent in 5-Base Windows\ maxHeightPixels 128:36:16\ shortLabel GC Percent\ spanList 5\ track gc5Base\ type wig 0 100\ viewLimits 30:70\ visibility hide\ windowingFunction Mean\ microsat Microsatellite bed 4 Microsatellites - Di-nucleotide and Tri-nucleotide Repeats 0 100 0 0 0 127 127 127 0 0 0\ This track displays regions that are likely to be useful as microsatellite\ markers. These are sequences of at least 15 perfect di-nucleotide and \ tri-nucleotide repeats and tend to be highly polymorphic in the\ population.\
\ \\ The data shown in this track are a subset of the Simple Repeats track, \ selecting only those \ repeats of period 2 and 3, with 100% identity and no indels and with\ at least 15 copies of the repeat. The Simple Repeats track is\ created using the \ Tandem Repeats Finder. For more information about this \ program, see Benson (1999).
\ \\ Tandem Repeats Finder 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 shows known protein-coding and non-protein-coding genes \ for organisms other than C. brenneri, 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. brenneri 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:
\ The Quality Scores track shows the sequencing quality score\ of each base in the assembly. The height at each position of the track \ indicates the quality of the base. \ When zoomed out to a large range, the heights reflect the averaged scores. \
\\ This track may 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.
\ \\ The quality scores were provided as part of the C. brenneri assembly. \ The database representation and graphical display code were written by\ Hiram Clawson.\ map 0 altColor 255,128,0\ autoScale Off\ color 0,128,255\ graphTypeDefault Bar\ gridDefault OFF\ group map\ longLabel C. brenneri Sequencing Quality Scores\ maxHeightPixels 128:36:16\ shortLabel Quality Scores\ spanList 1,1024\ track quality\ type wig 0 97\ visibility hide\ windowingFunction Mean\ 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 displays tRNA genes predicted by using \ tRNAscan-SE v.1.23. \
\\ tRNAscan-SE is an integrated program that uses tRNAscan (Fichant) and an A/B box motif detection \ algorithm (Pavesi) as pre-filters to obtain an initial list of tRNA candidates. \ The program then filters these candidates with a covariance model-based \ search program \ COVE (Eddy) to obtain a highly specific set of primary sequence \ and secondary structure predictions that represent 99-100% of true tRNAs \ with a false positive rate of fewer than 1 per 15 gigabases.
\\ Detailed tRNA annotations for eukaryotes, bacteria, and archaea are available at\ Genomic tRNA Database (GtRNAdb). \
\\ What does the tRNAscan-SE score mean? Anything with a score above 20 bits is likely to be\ derived from a tRNA, although this does not indicate whether the tRNA gene still encodes a \ functional tRNA molecule (i.e. tRNA-derived SINES probably do not function in the ribosome in translation).\ Vertebrate tRNAs with scores of >60.0 (bits) are likely to encode functional tRNA genes, and \ those with scores below ~45 have sequence or structural features that indicate they probably are\ no longer involved in translation. tRNAs with scores between 45-60 bits are in the "grey" zone, and may\ or may not have all the required features to be functional. In these cases, tRNAs should be inspected\ carefully for loss of specific primary or secondary structure features (usually in alignments with other\ genes of the same isotype), in order to make a better educated guess. These rough score range guides \ are not exact, nor are they based on specific biochemical studies of atypical tRNA features,\ so please treat them accordingly.\
\\ Please note that tRNA genes marked as "Pseudo" are low scoring predictions that are mostly pseudogenes or \ tRNA-derived elements. These genes do not usually fold into a typical cloverleaf tRNA secondary \ structure and the provided images of the predicted secondary structures may appear rotated.\
\ \\ Both tRNAscan-SE and GtRNAdb are maintained by the\ Lowe Lab at UCSC.\
\\ Cove-predicted tRNA secondary structures were rendered by NAVIEW (c) 1988 Robert E. Bruccoleri.\
\ \\ When making use of these data, please cite the following articles:
\\
Chan PP, Lowe TM. \
GtRNAdb: a database of transfer RNA genes detected in genomic sequence.\
Nucleic Acids Res. 2009 Jan;37(Database issue):D93-7.\
PMID: 18984615; PMC:
\
Eddy SR, Durbin R. \
\
RNA sequence analysis using covariance models.\
Nucleic Acids Res. 1994 Jun 11;22(11):2079-88.\
PMID: 8029015; PMC:
\ Fichant GA, Burks C. \ \ Identifying potential tRNA genes in genomic DNA sequences.\ J Mol Biol. 1991 Aug 5;220(3):659-71.\ PMID: 1870126\
\ \\
Lowe TM, Eddy SR. \
\
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.\
Nucleic Acids Res. 1997 Mar 1;25(5):955-64.\
PMID: 9023104; PMC:
\
Pavesi A, Conterio F, Bolchi A, Dieci G, Ottonello S.\
\
Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix\
analysis of transcriptional control regions.\
Nucleic Acids Res. 1994 Apr 11;22(7):1247-56.\
PMID: 8165140; 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 caePb1.fa -output wm_counts\ windowmasker -ustat wm_counts -sdust true -input caePb1.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\ chainPriPac1 P. pacificus Chain chain priPac1 P. pacificus (Feb. 2007 (WUGSC 5.0/priPac1)) Chained Alignments 0 122 100 50 0 255 240 200 1 0 0\ This track shows alignments of P. pacificus (priPac1, Feb. 2007 (WUGSC 5.0/priPac1)) to the\ C. brenneri genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ P. pacificus and C. brenneri 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\ P. pacificus assembly or an insertion in the C. brenneri\ 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. brenneri 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.
\ \\ Transposons that have been inserted since the P. pacificus/C. brenneri\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz using dynamic masking, and the transposons were then \ added back in. The resulting alignments were converted into psl format \ using the lavToPsl program. The axt alignments were fed into axtChain, which \ organizes all alignments between a single P. pacificus chromosome and a \ single C. brenneri 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.\ \ The following matrix was used:
\
\ \ \ Chains scoring below a threshold of 2000 were discarded; the remaining\ chains are displayed in this track. \ \\
\ A C G T \ A 91 -114 -31 -123 \ C -114 100 -125 -31 \ G -31 -125 100 -114 \ T -123 -31 -114 91
\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Repeat areas we marked in the genome with WindowMasker as\ developed by: Morgulis A, Gertz EM, Schäffer AA, Agarwala R.\
\\ 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:
\ 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\
\ \\
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:
\ This track shows the best P. pacificus/C. brenneri chain for \ every part of the C. brenneri genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The P. pacificus sequence used in this annotation is from\ the Feb. 2007 (WUGSC 5.0/priPac1) (priPac1) assembly.
\ \\ 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):
\\ Chains were derived from blastz 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.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ The browser display and database storage of the nets were made\ by Robert Baertsch and Jim Kent.
\ \\
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:
\ This track shows alignments of C. briggsae (cb3, Jan. 2007 (WUGSC 1.0/cb3)) to the\ C. brenneri genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ C. briggsae and C. brenneri 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\ C. briggsae assembly or an insertion in the C. brenneri\ 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. brenneri 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.
\ \\ Transposons that have been inserted since the C. briggsae/C. brenneri\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz using dynamic masking, and the transposons were then \ added back in. The resulting alignments were converted into psl format \ using the lavToPsl program. The axt alignments were fed into axtChain, which \ organizes all alignments between a single C. briggsae chromosome and a \ single C. brenneri 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.\ \ The following matrix was used:
\
\ \ \ Chains scoring below a threshold of 2000 were discarded; the remaining\ chains are displayed in this track. \ \\
\ A C G T \ A 91 -114 -31 -123 \ C -114 100 -125 -31 \ G -31 -125 100 -114 \ T -123 -31 -114 91
\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Repeat areas we marked in the genome with WindowMasker as\ developed by: Morgulis A, Gertz EM, Schäffer AA, Agarwala R.\
\\ 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:
\ 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\
\ \\
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:
\ This track shows the best C. briggsae/C. brenneri chain for \ every part of the C. brenneri genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The C. briggsae sequence used in this annotation is from\ the Jan. 2007 (WUGSC 1.0/cb3) (cb3) assembly.
\ \\ 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):
\\ Chains were derived from blastz 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.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ The browser display and database storage of the nets were made\ by Robert Baertsch and Jim Kent.
\ \\
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:
\ This track shows alignments of C. remanei (caeRem2, Mar. 2006 (WUGSC 1.0/caeRem2)) to the\ C. brenneri genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ C. remanei and C. brenneri 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\ C. remanei assembly or an insertion in the C. brenneri\ 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. brenneri 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.
\ \\ Transposons that have been inserted since the C. remanei/C. brenneri\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz using dynamic masking, and the transposons were then \ added back in. The resulting alignments were converted into psl format \ using the lavToPsl program. The axt alignments were fed into axtChain, which \ organizes all alignments between a single C. remanei chromosome and a \ single C. brenneri 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.\ \ The following matrix was used:
\
\ \ \ Chains scoring below a threshold of 2000 were discarded; the remaining\ chains are displayed in this track. \ \\
\ A C G T \ A 91 -114 -31 -123 \ C -114 100 -125 -31 \ G -31 -125 100 -114 \ T -123 -31 -114 91
\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Repeat areas we marked in the genome with WindowMasker as\ developed by: Morgulis A, Gertz EM, Schäffer AA, Agarwala R.\
\\ 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:
\ 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\
\ \\
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:
\ This track shows the best C. remanei/C. brenneri chain for \ every part of the C. brenneri genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The C. remanei sequence used in this annotation is from\ the Mar. 2006 (WUGSC 1.0/caeRem2) (caeRem2) assembly.
\ \\ 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):
\\ Chains were derived from blastz 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.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ The browser display and database storage of the nets were made\ by Robert Baertsch and Jim Kent.
\ \\
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:
\ This track shows alignments of C. elegans (ce4, Jan. 2007 (WS170/ce4)) to the\ C. brenneri genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ C. elegans and C. brenneri 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\ C. elegans assembly or an insertion in the C. brenneri\ 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. brenneri 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.
\ \\ Transposons that have been inserted since the C. elegans/C. brenneri\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz using dynamic masking, and the transposons were then \ added back in. The resulting alignments were converted into psl format \ using the lavToPsl program. The axt alignments were fed into axtChain, which \ organizes all alignments between a single C. elegans chromosome and a \ single C. brenneri 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.\ \ The following matrix was used:
\
\ \ \ Chains scoring below a threshold of 2000 were discarded; the remaining\ chains are displayed in this track. \ \\
\ A C G T \ A 91 -114 -31 -123 \ C -114 100 -125 -31 \ G -31 -125 100 -114 \ T -123 -31 -114 91
\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Repeat areas we marked in the genome with WindowMasker as\ developed by: Morgulis A, Gertz EM, Schäffer AA, Agarwala R.\
\\ 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:
\ 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\
\ \\
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 shows the best C. elegans/C. brenneri chain for \ every part of the C. brenneri genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The C. elegans sequence used in this annotation is from\ the Jan. 2007 (WS170/ce4) (ce4) assembly.
\ \\ 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):
\\ Chains were derived from blastz 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.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ The browser display and database storage of the nets were made\ by Robert Baertsch and Jim Kent.
\ \\
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:
\
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 dense\ blastCe4SG C. elegans Proteins psl protein C. elegans Proteins WS170 Mapped by Chained tBLASTn 3 250.2 0 0 0 127 127 127 0 0 0 http://ws170.wormbase.org/db/gene/gene?name=\ This track contains tBLASTn alignments of the peptides from the WormBase\ genes annotations on C. elegans version WS170 (UCSC ce4)
\ \\ tBLASTn is part of the NCBI Blast tool set. For more information on Blast, see\ Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. \ Basic local alignment search tool. \ J Mol Biol. 1990 Oct 5;215(3):403-410.
\\ Blat was written by Jim Kent. The remaining utilities \ used to produce this track were written by Jim Kent, Brian Raney or\ Hiram Clawson.
\ genes 1 blastRef ce4.blastSGRef01\ colorChromDefault off\ group genes\ longLabel C. elegans Proteins WS170 Mapped by Chained tBLASTn\ pred ce4.blastSGPep01\ priority 250.2\ shortLabel C. elegans Proteins\ track blastCe4SG\ type psl protein\ url http://ws170.wormbase.org/db/gene/gene?name=\ visibility pack\