\ This track shows chromosome bands annotated by \ FlyBase \ (D. melanogaster version 5.12).\
\\ Thanks to FlyBase for providing these annotations.\
\ \ map 1 altColor 200,150,150\ group map\ longLabel Chromosome Bands\ priority .1\ shortLabel Chromosome Band\ track cytoBand\ type bed 4 +\ visibility hide\ cytoBandIdeo Chromosome Band (Low-res) bed 4 + Chromosome Bands (Low-resolution for Chromosome Ideogram) 1 0.1 0 0 0 200 150 150 0 0 0 map 1 altColor 200,150,150\ group map\ longLabel Chromosome Bands (Low-resolution for Chromosome Ideogram)\ priority .1\ shortLabel Chromosome Band (Low-res)\ track cytoBandIdeo\ type bed 4 +\ visibility dense\ affyDrosDevSignal1 Affy Devel 0-2h wig -1019.0 2277.25 Affymetrix Drosophila Development Signal, 0-2 hours 0 1 50 50 130 152 152 192 0 0 0 regulation 0 color 50,50,130\ longLabel Affymetrix Drosophila Development Signal, 0-2 hours\ parent affyDrosDevSignal\ priority 1\ shortLabel Affy Devel 0-2h\ track affyDrosDevSignal1\ affyDrosDevTransfrags1 Affy Devel 0-2h bed 3 . Affymetrix Drosophila Development Transfrags, 0-2 hours 0 1 50 50 130 152 152 192 0 0 0 regulation 1 color 50,50,130\ longLabel Affymetrix Drosophila Development Transfrags, 0-2 hours\ parent affyDrosDevTransfrags\ priority 1\ shortLabel Affy Devel 0-2h\ track affyDrosDevTransfrags1\ bdtnpBcd2Fdr1 bcd AB 2 FDR 1% wig 0.0 40.39 BDTNP ChIP/chip: bicoid (bcd) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1% 3 1 0 150 0 127 202 127 0 0 0 regulation 0 color 0,150,0\ longLabel BDTNP ChIP/chip: bicoid (bcd) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1%\ parent bdtnpChipperViewbest1\ priority 3\ shortLabel bcd AB 2 FDR 1%\ subGroups factor=BCD class=ape1m view=best1 stage=s04\ track bdtnpBcd2Fdr1\ type wig 0.0 40.39\ pubsBlatPsl Indiv. Seq. Matches psl Individual Sequence Matches of One Selected Article from Sequences Track 0 1 0 115 70 127 185 162 0 0 0 pub 1 color 0,115,70\ configurable off\ configureByPopup off\ longLabel Individual Sequence Matches of One Selected Article from Sequences Track\ parent pubs off\ priority 1\ shortLabel Indiv. Seq. Matches\ track pubsBlatPsl\ type psl\ visibility hide\ bdtnpDnaseS5R9481 S5 repl. 1 bigWig 0 4448.18 BDTNP Chromatin Accessibility (DNase) Stage 5, Replicate 1 2 1 47 168 64 151 211 159 0 0 0 regulation 0 color 47,168,64\ longLabel BDTNP Chromatin Accessibility (DNase) Stage 5, Replicate 1\ parent bdtnpDnaseViewAcc\ shortLabel S5 repl. 1\ subGroups view=acc stage=s05 repl=r1\ track bdtnpDnaseS5R9481\ type bigWig 0 4448.18\ affyDrosDevSignal2 Affy Devel 2-4h wig -1019.0 2277.25 Affymetrix Drosophila Development Signal, 2-4 hours 0 2 50 50 140 152 152 197 0 0 0 regulation 0 color 50,50,140\ longLabel Affymetrix Drosophila Development Signal, 2-4 hours\ parent affyDrosDevSignal\ priority 2\ shortLabel Affy Devel 2-4h\ track affyDrosDevSignal2\ affyDrosDevTransfrags2 Affy Devel 2-4h bed 3 . Affymetrix Drosophila Development Transfrags, 2-4 hours 0 2 50 50 140 152 152 197 0 0 0 regulation 1 color 50,50,140\ longLabel Affymetrix Drosophila Development Transfrags, 2-4 hours\ parent affyDrosDevTransfrags\ priority 2\ shortLabel Affy Devel 2-4h\ track affyDrosDevTransfrags2\ bdtnpBcd2Fdr25 bcd AB 2 FDR 25% wig 0.0 40.39 BDTNP ChIP/chip: bicoid (bcd) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 25% 0 2 0 150 0 127 202 127 0 0 0 regulation 0 color 0,150,0\ longLabel BDTNP ChIP/chip: bicoid (bcd) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 25%\ parent bdtnpChipperViewbest25\ priority 4\ shortLabel bcd AB 2 FDR 25%\ subGroups factor=BCD class=ape1m view=best25 stage=s04\ track bdtnpBcd2Fdr25\ type wig 0.0 40.39\ refGene RefSeq Genes genePred refPep refMrna RefSeq Genes 1 2 12 12 120 133 133 187 0 0 0\ The RefSeq Genes track shows known D. melanogaster 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 D. melanogaster 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:
\ This track shows the locations of P and Minos transposable element insertions\ from the \ \ Gene Disruption Project,\ the ongoing collaboration of the Bellen, Hoskins and Spradling \ labs that began as the \ \ BDGP Gene Disruption Project.\
\ Triangular arrows indicate the approximate positions in the reference\ sequence at which P or Minos elements have been inserted. \ The direction of the arrow corresponds to the orientation of the\ insertion: right-pointing arrows indicate forward orientation;\ left-pointing arrows show reverse orientation. \ The item name indicates the strain that has a P or Minos insertion at\ that location. \ When a stock order number is available for the strain, a link is\ provided to the Bloomington stock center where the strain can be\ ordered. The project's strain library contains more than 7670 strains\ disrupting at least 5359 genes annotated by FlyBase. This track omits\ several strains whose insertion coordinates are not yet known.\ \
\ See the Gene Disruption Project Database for materials and methods.\ \
\ Thanks to the Gene Disruption Project. Please cite the Bellen et\ al. reference below when using strains from the collection.\
\ \\
Bellen HJ, Levis RW, Liao G, He Y, Carlson JW, Tsang G, Evans-Holm M, Hiesinger PR, Schulze KL,\
Rubin GM et al.\
\
The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila\
genes.\
Genetics. 2004 Jun;167(2):761-81.\
PMID: 15238527; PMC:
\
Metaxakis A, Oehler S, Klinakis A, Savakis C.\
\
Minos as a genetic and genomic tool in Drosophila melanogaster.\
Genetics. 2005 Oct;171(2):571-81.\
PMID: 15972463; PMC:
\ Bacterial artificial chromosomes (BACs) are a key part of many \ large-scale sequencing projects. A BAC typically consists of 50 - 300 kb of\ DNA. During the early phase of a sequencing project, it is common\ to sequence a single read (approximately 500 bases) off each end of\ a large number of BACs. Later on in the project, these BAC end reads\ can be mapped to the genome sequence.
\\ This track shows these mappings\ in cases where both ends could be mapped. These BAC end pairs can\ be useful for validating the assembly over relatively long ranges. In some\ cases, the BACs are useful biological reagents. This track can also be\ used for determining which BAC contains a given gene, useful information\ for certain wet lab experiments.
\\ The RPCI-98 \ and \ DrosBAC \ libraries, individual clones, and hybridization filters are available \ from the \ BACPAC \ Resources Center (BPRC) at Children's Hospital Oakland Research \ Institute (CHORI). \ Individual clones from the RPCI-98 library are named BACR01A01 - \ BACR48H12 (96-well format; R stands for EcoRI). \ Individual clones from the DrosBAC library are named BACN01A01 - \ BACN47H12 and BACH48A01 - BACH61H12 (N stands for NdeII; H stands for HinDIII).\
\\ In order to be included in this track, a \ valid pair of BAC end sequence alignments must be\ at least 25 kb but no more than 500 kb away from each other. \ The orientation of the first BAC end sequence must be "+" and\ the orientation of the second BAC end sequence must be "-".
\\ The scoring scheme used for this annotation assigns 1000 to an alignment \ when the BAC end pair aligns to only one location in the genome (after \ filtering). When a BAC end pair or clone aligns to multiple locations, the \ score is calculated as 1500/(number of alignments).
\ \\ BAC end sequences were downloaded from \ Genoscope \ (https://jacob.cea.fr/drf/ifrancoisjacob/english/Pages/Departments/Genoscope/Genoscope_s-bioinformatics-resources.aspx) \ and then placed on the assembled sequence using Jim Kent's \ blat program.\ Terry Furey's pslPairs program was used to identify paired end alignments.\
\ \\ The RPCI-98 \ BAC library was produced by BACPAC Resources, then at\ Roswell Park Cancer Institute and now at \ CHORI,\ in collaboration with the \ Berkeley Drosophila Genome Project.\ The \ DrosBAC \ library was made by Alain Billaud at \ CEPH \ (Centre d'Etude du Polymorphisme Humain) in a\ collaboration with the European Drosophila Genome Project co-ordinated\ by D. Glover.\ Thanks to Genoscope for providing the BAC end sequence files.
\ map 1 exonArrows off\ group map\ longLabel BAC End Pairs\ notNCBI .\ priority 15\ shortLabel BAC End Pairs\ track bacEndPairs\ type bed 6 +\ visibility hide\ bdtnpHb2Fdr25 hb AB 2 FDR 25% wig 0.0 40.39 BDTNP ChIP/chip: hunchback (hb) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 25% 0 15 0 150 0 127 202 127 0 0 0 regulation 0 color 0,150,0\ longLabel BDTNP ChIP/chip: hunchback (hb) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 25%\ parent bdtnpChipperViewother25\ priority 12\ shortLabel hb AB 2 FDR 25%\ subGroups factor=HB class=ape2g view=other25 stage=s04\ track bdtnpHb2Fdr25\ type wig 0.0 40.39\ bdtnpDnaseAccS14 S14 Regions bed 3 BDTNP Chromatin Accessibility (DNase) Stage 14, FDR 5% euchromatic accessible regions 4 15 109 57 160 182 156 207 0 0 0 regulation 1 color 109,57,160\ longLabel BDTNP Chromatin Accessibility (DNase) Stage 14, FDR 5% euchromatic accessible regions\ parent bdtnpDnaseViewRegions\ shortLabel S14 Regions\ subGroups view=regions stage=s14 repl=r3both\ track bdtnpDnaseAccS14\ bdtnpHb2S9Fdr25 hb AB2 S9 FDR25% bigWig 0.0 17.4 BDTNP ChIP/chip: hunchback (hb) antibody 2, stage 9 embryos, False Discovery Rate (FDR) 25% 0 16 0 150 0 127 202 127 0 0 0 regulation 0 color 0,150,0\ longLabel BDTNP ChIP/chip: hunchback (hb) antibody 2, stage 9 embryos, False Discovery Rate (FDR) 25%\ parent bdtnpChipperViewother25\ priority 12\ shortLabel hb AB2 S9 FDR25%\ subGroups factor=HB class=ape2g view=other25 stage=s09\ track bdtnpHb2S9Fdr25\ type bigWig 0.0 17.4\ bdtnpKni2Fdr1 kni AB 2 FDR 1% wig 0.0 40.39 BDTNP ChIP/chip: knirps (kni) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1% 3 17 0 150 0 127 202 127 0 0 0 regulation 0 color 0,150,0\ longLabel BDTNP ChIP/chip: knirps (kni) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1%\ parent bdtnpChipperViewbest1\ priority 15\ shortLabel kni AB 2 FDR 1%\ subGroups factor=KNI class=ape2g view=best1 stage=s04\ track bdtnpKni2Fdr1\ type wig 0.0 40.39\ bdtnpKni2Fdr25 kni AB 2 FDR 25% wig 0.0 40.39 BDTNP ChIP/chip: knirps (kni) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 25% 0 18 0 150 0 127 202 127 0 0 0 regulation 0 color 0,150,0\ longLabel BDTNP ChIP/chip: knirps (kni) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 25%\ parent bdtnpChipperViewbest25\ priority 16\ shortLabel kni AB 2 FDR 25%\ subGroups factor=KNI class=ape2g view=best25 stage=s04\ track bdtnpKni2Fdr25\ type wig 0.0 40.39\ bdtnpKni1Fdr1 kni AB 1 FDR 1% wig 0.0 40.39 BDTNP ChIP/chip: knirps (kni) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 1% 0 19 0 150 0 127 202 127 0 0 0 regulation 0 color 0,150,0\ longLabel BDTNP ChIP/chip: knirps (kni) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 1%\ parent bdtnpChipperViewother1\ priority 13\ shortLabel kni AB 1 FDR 1%\ subGroups factor=KNI class=ape2g view=other1 stage=s04\ track bdtnpKni1Fdr1\ type wig 0.0 40.39\ bdtnpKni1Fdr25 kni AB 1 FDR 25% wig 0.0 40.39 BDTNP ChIP/chip: knirps (kni) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 25% 0 20 0 150 0 127 202 127 0 0 0 regulation 0 color 0,150,0\ longLabel BDTNP ChIP/chip: knirps (kni) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 25%\ parent bdtnpChipperViewother25\ priority 14\ shortLabel kni AB 1 FDR 25%\ subGroups factor=KNI class=ape2g view=other25 stage=s04\ track bdtnpKni1Fdr25\ type wig 0.0 40.39\ bdtnpKr2Fdr1 Kr AB 2 FDR 1% wig 0.0 40.39 BDTNP ChIP/chip: Kruppel (Kr) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1% 3 21 0 150 0 127 202 127 0 0 0 regulation 0 color 0,150,0\ longLabel BDTNP ChIP/chip: Kruppel (Kr) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1%\ parent bdtnpChipperViewbest1\ priority 19\ shortLabel Kr AB 2 FDR 1%\ subGroups factor=KR class=ape2g view=best1 stage=s04\ track bdtnpKr2Fdr1\ type wig 0.0 40.39\ bdtnpKr2Fdr25 Kr AB 2 FDR 25% wig 0.0 40.39 BDTNP ChIP/chip: Kruppel (Kr) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 25% 0 22 0 150 0 127 202 127 0 0 0 regulation 0 color 0,150,0\ longLabel BDTNP ChIP/chip: Kruppel (Kr) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 25%\ parent bdtnpChipperViewbest25\ priority 20\ shortLabel Kr AB 2 FDR 25%\ subGroups factor=KR class=ape2g view=best25 stage=s04\ track bdtnpKr2Fdr25\ type wig 0.0 40.39\ phastConsElements15way 15 Insect El bed 5 . PhastCons Conserved Elements (12 Flies, Mosquito, Honeybee, Beetle) 1 23 110 10 40 182 132 147 0 0 0\ This track shows predictions of conserved elements produced by the phastCons\ program. PhastCons is part of the PHAST (PHylogenetic Analysis with\ Space/Time models) package. The predictions are based on a phylogenetic hidden\ Markov model (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.
\ \\ Best-in-genome pairwise alignments were generated for\ each species using blastz, followed by chaining and netting. A multiple\ alignment was then constructed from these pairwise alignments using multiz.\ Predictions of conserved elements were then obtained by running phastCons\ on the multiple alignments with the --most-conserved option.
\\ PhastCons constructs a two-state phylo-HMM with a state for conserved\ regions and a state for non-conserved regions. The two states share a\ single phylogenetic model, except that the branch lengths of the tree\ associated with the conserved state are multiplied by a constant scaling\ factor rho (0 <= rho <= 1). The free parameters of the\ phylo-HMM, including the scaling factor rho, are estimated from\ the data by maximum likelihood using an EM algorithm. This procedure is\ subject to certain constraints on the "coverage" of the genome by conserved\ elements and the "smoothness" of the conservation scores. Details can be\ found in Siepel et al. (2005).
\\ The predicted conserved 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 at UCSC using the following programs:\
\
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:
\
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\
\ \\
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 protein-coding genes annotated by \ FlyBase\ and the \ Drosophila Heterochromatin\ Genome Project (DHGP).\ Annotations on both heterochromatin and euchromatic sequences were \ downloaded from FlyBase\ D. melanogaster version 5.12.\
\ \\ Thanks to \ FlyBase \ and \ DHGP\ for providing these annotations.\
\ \\ Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM;\ FlyBase Consortium.\ FlyBase: genomes by the dozen.\ Nucleic Acids Res. 2007 Jan;35(Database issue):D486-91.\
\\ Smith CD, Shu S, Mungall CJ, Karpen GH.\ The Release 5.1 Annotation of Drosophila melanogaster \ Heterochromatin.\ Science. 2007 Jun 15;316(5831):1586-91. \
\ genes 1 color 0,100,180\ directUrl ../cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s\ group genes\ hgGene on\ hgsid on\ longLabel FlyBase Protein-Coding Genes\ priority 34\ shortLabel FlyBase Genes\ symbolTable flyBase2004Xref\ track flyBaseGene\ type genePred flyBasePep\ visibility pack\ flyBaseNoncoding FB Noncoding bed 12 . FlyBase Noncoding Genes 3 34.1 30 130 210 142 192 232 0 0 0\ This track shows non-protein-coding genes annotated by \ FlyBase\ and the \ Drosophila Heterochromatin\ Genome Project (DHGP).\ Annotations on both heterochromatin and euchromatic sequences were \ downloaded from FlyBase\ D. melanogaster version 5.12.\
\ \\ Thanks to \ FlyBase \ and \ DHGP\ for providing these annotations.\
\ \\ Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM;\ FlyBase Consortium.\ FlyBase: genomes by the dozen.\ Nucleic Acids Res. 2007 Jan;35(Database issue):D486-91.\
\\ Smith CD, Shu S, Mungall CJ, Karpen GH.\ The Release 5.1 Annotation of Drosophila melanogaster \ Heterochromatin.\ Science. 2007 Jun 15;316(5831):1586-91. \
\ genes 1 color 30,130,210\ group genes\ longLabel FlyBase Noncoding Genes\ noScoreFilter .\ priority 34.1\ shortLabel FB Noncoding\ symbolTable flyBase2004Xref\ track flyBaseNoncoding\ type bed 12 .\ visibility pack\ bdtnpFtz3Fdr1 ftz AB 3 FDR 1% wig 0.0 40.39 BDTNP ChIP/chip: fushi tarazu (ftz) antibody 3, stage 4-5 embryos, False Discovery Rate (FDR) 1% 3 35 200 150 0 227 202 127 0 0 0 regulation 0 color 200,150,0\ longLabel BDTNP ChIP/chip: fushi tarazu (ftz) antibody 3, stage 4-5 embryos, False Discovery Rate (FDR) 1%\ parent bdtnpChipperViewbest1\ priority 31\ shortLabel ftz AB 3 FDR 1%\ subGroups factor=FTZ class=app view=best1 stage=s04\ track bdtnpFtz3Fdr1\ type wig 0.0 40.39\ bdtnpFtz3Fdr25 ftz AB 3 FDR 25% wig 0.0 40.39 BDTNP ChIP/chip: fushi tarazu (ftz) antibody 3, stage 4-5 embryos, False Discovery Rate (FDR) 25% 0 36 200 150 0 227 202 127 0 0 0 regulation 0 color 200,150,0\ longLabel BDTNP ChIP/chip: fushi tarazu (ftz) antibody 3, stage 4-5 embryos, False Discovery Rate (FDR) 25%\ parent bdtnpChipperViewbest25\ priority 32\ shortLabel ftz AB 3 FDR 25%\ subGroups factor=FTZ class=app view=best25 stage=s04\ track bdtnpFtz3Fdr25\ type wig 0.0 40.39\ bdtnpH2Fdr1 h AB 2 FDR 1% wig 0.0 40.39 BDTNP ChIP/chip: hairy (h) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1% 3 37 200 150 0 227 202 127 0 0 0 regulation 0 color 200,150,0\ longLabel BDTNP ChIP/chip: hairy (h) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1%\ parent bdtnpChipperViewbest1\ priority 35\ shortLabel h AB 2 FDR 1%\ subGroups factor=H class=app view=best1 stage=s04\ track bdtnpH2Fdr1\ type wig 0.0 40.39\ bdtnpH2Fdr25 h AB 2 FDR 25% wig 0.0 40.39 BDTNP ChIP/chip: hairy (h) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 25% 0 38 200 150 0 227 202 127 0 0 0 regulation 0 color 200,150,0\ longLabel BDTNP ChIP/chip: hairy (h) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 25%\ parent bdtnpChipperViewbest25\ priority 36\ shortLabel h AB 2 FDR 25%\ subGroups factor=H class=app view=best25 stage=s04\ track bdtnpH2Fdr25\ type wig 0.0 40.39\ bdtnpH1Fdr1 h AB 1 FDR 1% wig 0.0 40.39 BDTNP ChIP/chip: hairy (h) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 1% 0 39 200 150 0 227 202 127 0 0 0 regulation 0 color 200,150,0\ longLabel BDTNP ChIP/chip: hairy (h) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 1%\ parent bdtnpChipperViewother1\ priority 33\ shortLabel h AB 1 FDR 1%\ subGroups factor=H class=app view=other1 stage=s04\ track bdtnpH1Fdr1\ type wig 0.0 40.39\ bdtnpH1Fdr25 h AB 1 FDR 25% wig 0.0 40.39 BDTNP ChIP/chip: hairy (h) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 25% 0 40 200 150 0 227 202 127 0 0 0 regulation 0 color 200,150,0\ longLabel BDTNP ChIP/chip: hairy (h) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 25%\ parent bdtnpChipperViewother25\ priority 34\ shortLabel h AB 1 FDR 25%\ subGroups factor=H class=app view=other25 stage=s04\ track bdtnpH1Fdr25\ type wig 0.0 40.39\ bdtnpPrd1Fdr1 prd AB 1 FDR 1% wig 0.0 40.39 BDTNP ChIP/chip: paired (prd) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 1% 3 41 200 150 0 227 202 127 0 0 0 regulation 0 color 200,150,0\ longLabel BDTNP ChIP/chip: paired (prd) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 1%\ parent bdtnpChipperViewbest1\ priority 37\ shortLabel prd AB 1 FDR 1%\ subGroups factor=PRD class=app view=best1 stage=s04\ track bdtnpPrd1Fdr1\ type wig 0.0 40.39\ bdtnpPrd1Fdr25 prd AB 1 FDR 25% wig 0.0 40.39 BDTNP ChIP/chip: paired (prd) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 25% 0 42 200 150 0 227 202 127 0 0 0 regulation 0 color 200,150,0\ longLabel BDTNP ChIP/chip: paired (prd) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 25%\ parent bdtnpChipperViewbest25\ priority 38\ shortLabel prd AB 1 FDR 25%\ subGroups factor=PRD class=app view=best25 stage=s04\ track bdtnpPrd1Fdr25\ type wig 0.0 40.39\ bdtnpPrd2Fdr1 prd AB 2 FDR 1% wig 0.0 40.39 BDTNP ChIP/chip: paired (prd) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1% 0 43 200 150 0 227 202 127 0 0 0 regulation 0 color 200,150,0\ longLabel BDTNP ChIP/chip: paired (prd) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 1%\ parent bdtnpChipperViewother1\ priority 39\ shortLabel prd AB 2 FDR 1%\ subGroups factor=PRD class=app view=other1 stage=s04\ track bdtnpPrd2Fdr1\ type wig 0.0 40.39\ bdtnpPrd2Fdr25 prd AB 2 FDR 25% wig 0.0 40.39 BDTNP ChIP/chip: paired (prd) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 25% 0 44 200 150 0 227 202 127 0 0 0 regulation 0 color 200,150,0\ longLabel BDTNP ChIP/chip: paired (prd) antibody 2, stage 4-5 embryos, False Discovery Rate (FDR) 25%\ parent bdtnpChipperViewother25\ priority 40\ shortLabel prd AB 2 FDR 25%\ subGroups factor=PRD class=app view=other25 stage=s04\ track bdtnpPrd2Fdr25\ type wig 0.0 40.39\ bdtnpRun1Fdr1 run AB 1 FDR 1% wig 0.0 40.39 BDTNP ChIP/chip: runt (run) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 1% 3 45 200 150 0 227 202 127 0 0 0 regulation 0 color 200,150,0\ longLabel BDTNP ChIP/chip: runt (run) antibody 1, stage 4-5 embryos, False Discovery Rate (FDR) 1%\ parent bdtnpChipperViewbest1\ priority 41\ shortLabel run AB 1 FDR 1%\ subGroups factor=RUN class=app view=best1 stage=s04\ track bdtnpRun1Fdr1\ type wig 0.0 40.39\ nscanPasaGene N-SCAN genePred nscanPasaPep N-SCAN PASA-EST Gene Predictions 0 45.1 34 139 34 144 197 144 0 0 0\ This track shows gene predictions using the N-SCAN gene structure prediction\ software provided by the Computational Genomics Lab at Washington University \ in St. Louis, MO, USA.\
\ \\ N-SCAN PASA-EST combines EST alignments into N-SCAN. Similar to the conservation\ sequence models in TWINSCAN, separate probability models are developed for EST\ alignments to genomic sequence in exons, introns, splice sites and UTRs,\ reflecting the EST alignment patterns in these regions. N-SCAN PASA-EST is more\ accurate than N-SCAN while retaining the ability to discover novel genes to\ which no ESTs align.\
\\ In N-SCAN PASA-EST, cDNA sequences were clustered using the PASA program\ beforehand. PASA, the Program to Assemble Spliced Alignments, was created by\ Brian Haas at TIGR. The algorithm assembles clusters of overlapping transcript\ alignments (ESTs and full-length cDNAs) into maximal alignment assemblies,\ thereby comprehensively incorporating all available transcript data and\ capturing subtle splicing variations.\
\\ The PASA clusters were used as 'EST' sequences in N-SCAN PASA-EST. The\ resulting gene models were updated with the input PASA clusters using the\ assembly tool of the PASA pipeline. These updates consist of automatically\ generated alternative splices, UTR features and sometimes merging of two gene\ models. In addition, PASA assigned open reading frames to clusters that did\ not overlap a gene prediction, but that did contain a full length cDNA, and\ output them as 'novel genes'. Note that PASA does not use any cDNA annotation\ from input but assigns the ORF itself.\
\\ No manual annotation was performed to generate any of the gene models. The\ high accuracy of the set is in part due to the large number of available ESTs\ and full length cDNAs.\
\\ Drosophila N-SCAN PASA uses D. erecta (droEre2) and \ D. pseudoobscura (dp4) as informants.\
\ \\ Thanks to Michael Brent's Computational Genomics Group at Washington \ University St. Louis for providing these data.\
\\ Special thanks for this implementation of N-SCAN to Aaron Tenney in\ the Brent lab, and Robert Zimmermann, currently at Max F. Perutz\ Laboratories in Vienna, Austria.\
\ \ \\ Gross SS, Brent MR.\ \ Using multiple alignments to improve gene prediction.\ J Comput Biol. 2006 Mar;13(2):379-93.\ PMID: 16597247\
\ \\
Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM,\
Rusch DB, Town CD et al.\
\
Improving the Arabidopsis genome annotation using maximal transcript \
alignment assemblies.\
Nucleic Acids Res. 2003 Oct 1;31(19):5654-66.\
PMID: 14500829; PMC:
\ Korf I, Flicek P, Duan D, Brent MR.\ \ Integrating genomic homology into gene structure prediction.\ Bioinformatics. 2001;17 Suppl 1:S140-8.\ PMID: 11473003\
\ \\
van Baren MJ, Brent MR.\
\
Iterative gene prediction and pseudogene removal improves genome annotation.\
Genome Res. 2006 May;16(5):678-85.\
PMID: 16651666; PMC:
\ This track shows alignments between D. melanogaster 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 \ D. melanogaster 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,\ click \ here.\
\ \\ 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, D. melanogaster 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 RNA secondary structure predictions made with the\ EvoFold program, a comparative method that exploits the evolutionary signal\ of genomic multiple-sequence alignments for identifying conserved\ functional RNA structures.
\ \\ Track elements are labeled using the convention ID_strand_score.\ When zoomed out beyond the base level, secondary structure prediction regions\ are indicated by blocks, with the stem-pairing regions shown in a darker shade \ than unpaired regions. Arrows indicate the predicted strand.\ When zoomed in to the base level, the specific secondary structure predictions \ are shown in parenthesis format. The confidence score for each position is\ indicated in grayscale, with darker shades corresponding to higher scores.\
\ The details page for each track element shows the predicted secondary\ structure (labeled SS anno), together with details of the\ multiple species alignments at that location. Substitutions relative\ to the Drosophila melanogaster sequence are color-coded\ according to their compatibility with the predicted secondary\ structure (see the color legend on the details page). Each prediction\ is assigned an overall score and a sequence of position-specific\ scores. The overall score measures evidence for any functional RNA\ structures in the given region, while the position-specific scores (0\ - 9) measure the confidence of the base-specific\ annotations. Base-pairing positions are annotated with the same pair\ symbol. The offsets are provided to ease visual navigation of\ the alignment in terms of the D. melanogaster sequence. The\ offset is calculated (in units of ten) from the start position of the\ element on the positive strand or from the end position when on the\ negative strand.
\\ The graphical display may be filtered to show only those track elements \ with scores that meet or exceed a certain threshhold. To set a \ threshhold, type the minimum score into the text box at the top of the \ description page.
\ \\ Evofold makes use of phylogenetic stochastic context-free grammars\ (phylo-SCFGs), which are combined probabilistic models of RNA\ secondary structure and primary sequence evolution. The predictions\ consist of both a specific RNA secondary structure and an overall\ score. The overall score is essentially a log-odd score between a\ phylo-SCFG modeling the constrained evolution of stem-pairing regions\ and one which only models unpaired regions.
\\ The predictions for this track were based on the conserved elements of\ a 12-way Drosophila alignment of the D. melanogaster\ (dm2), D. simulans (droSim1), D. sechellia\ (droSec1), D. yakuba (droYak2), D. erecta (droEre2),\ D. ananassae (droAna3), D. pseudoobscura (dp4),\ D. persimilis (droPer1), D. willistoni (droWil1),\ D. virilis (droVir3), D. mojavensis (droMoj3), and\ D. grimshawi (droGri2) assemblies. The 12-way\ Drosophila alignment was extracted from a 15-way insect\ alignment, which is the one displayed in the Conservation track.
\ \\ The EvoFold program and browser track were developed by \ Jakob Skou Pedersen.
\ \\
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S,\
Deoras AN et al.\
\
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.\
Nature. 2007 Nov 8;450(7167):219-32.\
PMID: 17994088; PMC:
\
Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W,\
Haussler D.\
\
Identification and classification of conserved RNA secondary structures in the human genome.\
PLoS Comput Biol. 2006 Apr;2(4):e33.\
PMID: 16628248; PMC:
\ Knudsen B, Hein J.\ RNA secondary structure prediction using stochastic context-free\ grammars and evolutionary history.\ Bioinformatics. 1999 Jun;15(6):446-54.\ PMID: 10383470\
\ \\
Pedersen JS, Meyer IM, Forsberg R, Simmonds P, Hein J.\
A comparative method for finding and folding RNA secondary\
structures within protein-coding regions.\
Nucleic Acids Res. 2004;32(16):4925-36.\
PMID: 15448187; 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:
\ This track shows an estimate of RNA abundance (transcription) \ over the first 24 hours of D. melanogaster development in \ two hour increments, measured by a tiling array as described in \ Manak et al. (2006) (see References).\ Composite signals are shown in\ separate subtracks for each of the twelve timepoints.
\ \\ The subtracks within this composite annotation track\ may be configured in a variety of ways to highlight different aspects of the \ displayed data. The graphical configuration options for the subtracks \ are shown at the top of the track description page, followed by a list of \ subtracks. To show only selected subtracks, uncheck the boxes next to \ the tracks that you wish to hide. \ For more information about the graphical configuration options, click the \ Graph\ configuration help link.
\\ Color differences among the subtracks are arbitrary. They provide a\ visual cue for distinguishing between the different timepoints.
\ \\ The data were processed into signal and transfrags as described in \ Cheng et al. (2005) and Kampa et al. (2004). \ The data from replicate arrays were quantile-normalized and all arrays\ were scaled to a median array intensity of 25. Within a sliding 101\ bp window centered on each probe, an estimate of RNA abundance\ (signal) was found by calculating the median of all pairwise average\ PM-MM values, where PM is a perfect match and MM is a mismatch. This data \ set was originally created for dm2(BDGP R4) and then lifted over to dm3(BDGP R5).\
\ \\ Samples were hybridized\ to duplicate arrays (three technical replicates). Transcribed regions\ were generated from the composite signal track by merging genomic positions\ to which probes are mapped. This merging was based on a 5% false\ positive rate cutoff in negative bacterial controls, a maximum\ gap (MaxGap) of 50 base-pairs and minimum run (MinRun) of 90 base-pairs (see\ the Affy TransFrags track for the merged regions).\ \
\ \\ These data were generated and analyzed by the Tom Gingeras group at \ Affymetrix.
\ \\ Please see the \ Affymetrix Transcriptome site for a project overview and\ additional references to Affymetrix tiling array publications.
\ \\ Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G\ et al.\ \ Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution.\ Science. 2005 May 20;308(5725):1149-54.\ PMID: 15790807\
\ \\
Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, Drenkow J, Piccolboni A, Bekiranov\
S, Helt G et al.\
\
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and\
22.\
Genome Res. 2004 Mar;14(3):331-42.\
PMID: 14993201; PMC:
\ Manak JR, Dike S, Sementchenko V, Kapranov P, Biemar F, Long J, Cheng J, Bell I, Ghosh S, Piccolboni\ A et al.\ \ Biological function of unannotated transcription during the early development of Drosophila\ melanogaster.\ Nat Genet. 2006 Oct;38(10):1151-8.\ PMID: 16951679\
\ regulation 0 autoScale off\ compositeTrack on\ group regulation\ longLabel Affymetrix Drosophila Development Signal\ maxHeightPixels 128:16:16\ priority 70.01\ shortLabel Affy Signal\ spanList 1\ track affyDrosDevSignal\ type wig -1019.0 2277.25\ viewLimits 0:25\ visibility hide\ affyDrosDevTransfrags Affy Transfrags bed 3 . Affymetrix Drosophila Development Transfrags 0 70.02 0 0 0 127 127 127 0 0 0\ This track shows the location of sites showing transcription \ over the first 24 hours of D. melanogaster development in \ two hour increments, measured by a tiling array as described in \ Manak et al. (2006) (see References).\ Clustered sites are shown in\ separate subtracks for each of the twelve timepoints.
\ \\ To show only selected subtracks, uncheck the boxes next to \ the tracks that you wish to hide. \
\ Color differences among the subtracks are arbitrary. They provide a\ visual cue for distinguishing between the different timepoints.
\ \\ The data were processed into signal and transfrags as described in \ Cheng et al. (2005) and Kampa et al. (2004). \ The data from replicate arrays were quantile-normalized and all arrays\ were scaled to a median array intensity of 25. Within a sliding 101\ bp window centered on each probe, an estimate of RNA abundance\ (signal) was found by calculating the median of all pairwise average\ PM-MM values, where PM is a perfect match and MM is a mismatch.\ This data set was originally created for dm2(BDGP R4) and then lifted over to dm3(BDGP R5).
\ \\ Samples were hybridized\ to duplicate arrays (three technical replicates). Transcribed regions\ (see the Affy Signal track) \ were generated from the composite signal track by merging genomic positions\ to which probes are mapped. This merging was based on a 5% false\ positive rate cutoff in negative bacterial controls, a maximum\ gap (MaxGap) of 50 base-pairs and minimum run (MinRun) of 90 base-pairs.\ \
\ These data were generated and analyzed by the Tom Gingeras group at \ Affymetrix.
\ \\ Please see the \ Affymetrix Transcriptome site for a project overview and\ additional references to Affymetrix tiling array publications.
\ \\ Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G\ et al.\ \ Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution.\ Science. 2005 May 20;308(5725):1149-54.\ PMID: 15790807\
\ \\
Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, Drenkow J, Piccolboni A, Bekiranov\
S, Helt G et al.\
\
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and\
22.\
Genome Res. 2004 Mar;14(3):331-42.\
PMID: 14993201; PMC:
\ Manak JR, Dike S, Sementchenko V, Kapranov P, Biemar F, Long J, Cheng J, Bell I, Ghosh S, Piccolboni\ A et al.\ \ Biological function of unannotated transcription during the early development of Drosophila\ melanogaster.\ Nat Genet. 2006 Oct;38(10):1151-8.\ PMID: 16951679\
\ regulation 1 compositeTrack on\ group regulation\ longLabel Affymetrix Drosophila Development Transfrags\ priority 70.02\ shortLabel Affy Transfrags\ track affyDrosDevTransfrags\ type bed 3 .\ visibility hide\ bdtnpDnaseViewAcc Accessibility bed 3 Berkeley Drosophila Transcription Network Project Chromatin Accessibility (DNase) 2 70.9 0 0 0 127 127 127 0 0 0 regulation 1 autoScale off\ longLabel Berkeley Drosophila Transcription Network Project Chromatin Accessibility (DNase)\ maxHeightPixels 100:30:10\ parent bdtnpDnase\ shortLabel Accessibility\ track bdtnpDnaseViewAcc\ view acc\ viewLimits 0:150\ visibility full\ bdtnpDnase BDTNP DNase Accs bed 3 Berkeley Drosophila Transcription Network Project Chromatin Accessibility (DNase) 3 70.9 0 0 0 127 127 127 0 0 0\ This track shows the accessibility of genomic DNA to DNase I digestion\ in the D. melanogaster embryo for five stages of development: 5, 9,\ 10, 11 and 14 (Thomas et al.). These data have been used to show the\ dynamics of chromatin accessibility during embryogenesis (Thomas et\ al) and that chromatin accessibility plays a dominant role in\ determining the widespread, overlapping patterns of binding by\ functionally distinct transcription factors in Drosophila embryos (Li\ et al.; Kaplan et al.).
\ \\ Subtracks are provided showing either the density of DNA sequence tags\ in 75 bp windows across the genome or the locations of 5% FDR\ accessible regions. DNA sequence tag density data for independent\ replica for each stage are provided, though by default only one\ replica is shown. The DNA tag density subtracks are by default shown\ in "full" and the locations of 5% FDR regions that are concordant\ in both replicas are shown in "squish". Data for each stage is shown in\ a different color: green for stage 5, orange for stage 9, red for\ stage 10, light blue for stage 11 and purple for stage 14.
\\ The graphical configuration options for the subtracks are shown at the\ top of the track controls page, followed by a list of subtracks. To\ show only selected subtracks, uncheck the boxes next to the tracks\ that you wish to hide. For more information about the graphical\ configuration options, click the Graph configuration help link.
\ \\ One hour collections of wild type embryos were aged to the appropriate\ developmental stage and then nuclei were isolated and briefly digested\ with DNase I. The DNA released by digestion was size fractionated\ through a sucrose gradient to capture 100 - 400 bp fragments, which\ were then used to generate an average of ~14 million sequence tags per\ sample to the Drosophila genome with an Illumina GA2. \ The data were analyzed to determine short genomic regions that are\ accessible to digestion at a 5% false discovery rate; see Thomas\ et al. for further details.
\ \\
Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB.\
\
Quantitative models of the mechanisms that control genome-wide patterns of transcription factor\
binding during early Drosophila development.\
PLoS Genet. 2011 Feb 3;7(2):e1001290.\
PMID: 21304941; PMC:
\
Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD.\
\
The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila\
transcription factor binding.\
Genome Biol. 2011;12(4):R34.\
PMID: 21473766; PMC:
\
Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A,\
Celniker SE et al.\
\
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development.\
Genome Biol. 2011;12(5):R43.\
PMID: 21569360; PMC:
\ This track shows an estimate of the binding activity of 24 \ transcription factors in the D. melanogaster embryo. \ Chromatin immunoprecipitation and whole-genome tiling arrays \ (ChIP/chip) were used (see Li, MacArthur et al.) \ to map the genomic regions bound by \ 22 sequence specific transcription factors\ and two general transcription factors: TFIIB and the transcriptionally\ active phosphorylated form of RNA polymerase II.\ The sequence specific factors (except for \ Zeste), described in the table below, fall into three \ regulatory classes: anterior-posterior (A-P) early, A-P pair rule, and\ dorsal-ventral (D-V).\ Data for all proteins except Zeste are for stage 4-5 blastoderm\ embryos. Data for Zeste are for stage 11 embryos.\ Enrichment factors (1 = no enrichment) are shown in separate subtracks \ for 36 antibodies at false discovery rates (FDR) of 1% and 25%.\
\| Seq. Specific Factor | \Symbol | DNA binding domain | Regulatory Class |
|---|---|---|---|
| Bicoid | \bcd | homeodomain | A-P early maternal |
| Caudal | \cad | homeodomain | A-P early maternal |
| Giant | \gt | b-zip domain | A-P early gap |
| Hunchback | \hb | C2H2 Zinc finger | A-P early gap |
| Knirps | \kni | receptor Zinc finger | A-P early gap |
| Krüppel | \Kr | C2H2 Zinc finger | A-P early gap |
| Huckebein | \hkb | C2H2 Zinc finger | A-P early terminal |
| Tailless | \tll | receptor Zinc finger | A-P early terminal |
| Dichaete | \D | HMG/SOX class | A-P early gap-like |
| Fushi tarazu | \ftz | homeodomain | A-P pair rule |
| Hairy | \h | bHLH | A-P pair rule |
| Paired | \prd | homeodomain / paired domain | A-P pair rule |
| Runt | \run | runt domain | A-P pair rule |
| Sloppy paired 1 | \slp1 | forkhead domain | A-P pair rule |
| Daughterless | \da | bHLH | D-V maternal |
| Dorsal | \dl | NFkB/rel | D-V maternal |
| Mothers against dpp | \mad | SMAD-MH1 | D-V zygotic |
| Medea | \med | SMAD-MH1 | D-V zygotic |
| Schnurri | \shn | C2H2 Zinc finger | D-V zygotic |
| Snail | \sna | C2H2 Zinc finger | D-V zygotic |
| Twist | \twi | bHLH | D-V zygotic |
| Zeste | \z | unique | ubiquitous |
\ By default, values are displayed in grayscale ("dense" mode)\ instead of graphing ("full" mode), and only 24 of the 72\ subtracks are shown: only those with FDR of 1% and only one antibody\ per factor (the antibody with the most bound regions at FDR of 1%). \ To change the configuration, click on the blue or gray\ button to the left of the track or click on the track title in the \ controls below the image.\
\\ The subtracks within this composite annotation track\ may be configured in a variety of ways to highlight different aspects of the \ displayed data. The graphical configuration options for the subtracks \ are shown at the top of the track controls page, followed by a list of \ subtracks. To show only selected subtracks, uncheck the boxes next to \ the tracks that you wish to hide. \ For more information about the graphical configuration options, click the \ Graph\ configuration help link.
\\ Subtracks are colored according to regulatory class: \ green for A-P early,\ orange for A-P pair rule,\ blue for D-V,\ brown for stage 11 zeste, and\ red for general transcription factors.
\ \\ Where practicable two antibody preparations that were independently\ purified against nonoverlapping epitopes were used. \ For each purified antibody, two independent replicates of three\ different sample types were analyzed on separate arrays:\
\ Thanks to the \ Berkeley Drosophila \ Transcription Network Project's \ In Vivo DNA Binding collaboration,\ and Stewart MacArthur and Mark Biggin in particular, for these data.\ \ \
\
Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M,\
Luengo Hendriks CL et al.\
\
Transcription factors bind thousands of active and inactive regions in the Drosophila\
blastoderm.\
PLoS Biol. 2008 Feb;6(2):e27.\
PMID: 18271625; PMC:
\
MacArthur S, Li XY, Li J, Brown JB, Chu HC, Zeng L, Grondona BP, Hechmer A, Simirenko L,\
Keränen SV et al.\
\
Developmental roles of 21 Drosophila transcription factors are determined by quantitative\
differences in binding to an overlapping set of thousands of genomic regions.\
Genome Biol. 2009;10(7):R80.\
PMID: 19627575; PMC:
\
Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB.\
\
Large-scale turnover of functional transcription factor binding sites in Drosophila.\
PLoS Comput Biol. 2006 Oct;2(10):e130.\
PMID: 17040121; PMC:
\
Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A,\
Celniker SE et al.\
\
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development.\
Genome Biol. 2011;12(5):R43.\
PMID: 21569360; PMC:
\ This track shows alignments between D. melanogaster 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,\ click \ here.\
\ \\ 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, D. melanogaster 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:
\ The mRNA track shows alignments between D. melanogaster 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, click \ here.\
\ \\ GenBank D. melanogaster 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 draft assembly of the D. melanogaster genome. \ \ Whole-genome shotgun reads were assembled into contigs. When possible, \ contigs were grouped into scaffolds (also known as "supercontigs").\ The order, orientation and gap sizes between contigs within a scaffold are\ based on paired-end read evidence.
\\ Locations of contigs and scaffolds were deduced from runs of Ns in the\ assembled sequence. A run of Ns of more than 50000 bases\ was assumed to be a gap between scaffolds, and a run of Ns between\ 20 and 50000 was assumed to be a gap\ between contigs.
\\ 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.
\\ All components within this track are of fragment type "D": \ Draft.
\ map 1 altColor 230,170,40\ color 150,100,30\ group map\ longLabel Assembly from Fragments\ shortLabel Assembly\ track gold\ type bed 3 +\ visibility hide\ augustusGene AUGUSTUS genePred AUGUSTUS ab initio gene predictions v3.1 0 100 12 105 0 133 180 127 0 0 0\ 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\ contrastGene CONTRAST coloredExon CONTRAST Gene Predictions 0 100 34 34 139 144 144 197 0 0 0\ This track shows protein-coding gene predictions generated by \ CONTRAST. \ Each predicted exon is colored according to confidence level: green (high\ confidence), orange (medium confidence), or red (low confidence).\
\ \\ CONTRAST predicts protein-coding genes from a multiple genomic\ alignment using a combination of discriminative machine learning techniques. A two-stage approach is used, in which output from local classifiers is combined with a global model of gene structure. CONTRAST is trained using a novel procedure designed to\ maximize expected coding region boundary detection accuracy.\ \
\ Please see the \ CONTRAST web site for details on how these predictions were generated and an estimate of accuracy. \ \
\ Thanks to Samuel Gross of the \ Batzoglou lab at Stanford University for providing these predictions.\ \
\
Gross SS, Do CB, Sirota M, Batzoglou S.\
CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo\
gene prediction.\
Genome Biol. 2007;8(12):R269.\
PMID: 18096039; 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 dm3 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:
\ 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 known, it is a bridged gap and a white line is drawn \ through the black box representing the gap.\
\\ This assembly was sequenced with paired reads taken from\ plasmids of various sizes.\ Overlapping reads were merged into contigs,\ and pairing information was then used to join the contigs into scaffolds.\ The gap sizes are estimated from the size of the \ plasmids,\ with a minimum gap size of 20.\
\ \This assembly contains the following 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\ 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\ blastHg18KG Human Proteins psl protein Human Proteins Mapped by Chained tBLASTn 0 100 0 0 0 127 127 127 0 0 0\ This track contains tBLASTn alignments of the peptides from the predicted and \ known genes identified in the hg18 UCSC Genes track.
\ \\ 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 or Brian Raney.
\ genes 1 blastRef hg18.blastKGRef04\ colorChromDefault off\ group genes\ longLabel Human Proteins Mapped by Chained tBLASTn\ pred hg18.blastKGPep04\ shortLabel Human Proteins\ track blastHg18KG\ type psl protein\ visibility hide\ 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 a measure of evolutionary conservation in \ twelve Drosophila species, mosquito, honeybee and red flour beetle,\ based on a phylogenetic hidden Markov model (phastCons).\ Multiz alignments of the following assemblies were used to generate this\ annotation: \
\ In full and pack display modes, conservation scores are displayed as\ a "wiggle" (histogram), where the height reflects the \ size of the score. Pairwise alignments of each \ species to the D. melanogaster genome are displayed below 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.
\\ The conservation wiggle 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.
\\ Checkboxes in the track configuration section allow excluding\ species from the pairwise display; however, this does not remove them\ from the conservation score display.\ To view detailed information about the alignments at a specific\ position, zoom in the display 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 D. melanogaster sequence at those \ alignment positions relative to the longest non-D. melanogaster sequence. \ If there is sufficient space in the display, the size of the gap is shown; \ if not, and if the gap size is a multiple of 3, a "*" is displayed, \ otherwise "+" is shown.
\\ 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:\ \
\ \ \\
\ Gene Track Species \ FlyBase Genes D. melanogaster \ mRNAs D. simulans, D. yakuba,\ A. gambiae, A. mellifera \ not translated All other species
\ Best-in-genome pairwise alignments were generated for each species \ using blastz, followed by chaining and netting. The pairwise alignments\ were then multiply aligned using the multiz program, \ according to this topology:\
\
(((((((((dm3 (droSim1 droSec1))\
(droYak2 droEre2)) droAna3)\
(dp4 droPer1)) droWil1)\
((droVir3 droMoj3) droGri2))\
anoGam1) apiMel3) triCas2)\
\
The resulting multiple alignments were then assigned \
conservation scores by phastCons.\
The phastCons parameters for the 15-way Drosophila annotations are: \ expected-length = 23.8; target-coverage = 0.393; rho is set to the \ default value = 0.3.
\\ 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. Note that, unlike many\ conservation-scoring programs, phastCons does not rely on a sliding window\ of fixed size, so 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).
\\ PhastCons currently treats alignment gaps as missing data, which\ sometimes has the effect of producing undesirably high conservation scores\ in gappy regions of the alignment. We are looking at several possible ways\ of improving the handling of alignment gaps.
\ \This track was created at UCSC using the following programs:\
\ 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\
\ \\
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\
\ \\
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 literature-curated regulatory regions, transcription\ factor binding sites, and regulatory polymorphisms from\ ORegAnno (Open Regulatory Annotation). For more detailed\ information on a particular regulatory element, follow the link to ORegAnno\ from the details page. \ \
\ \The display may be filtered to show only selected region types, such as:
\ \To exclude a region type, uncheck the appropriate box in the list at the top of \ the Track Settings page.
\ \\ An ORegAnno record describes an experimentally proven and published regulatory\ region (promoter, enhancer, etc.), transcription factor binding site, or\ regulatory polymorphism. Each annotation must have the following attributes:\
\ ORegAnno core team and principal contacts: Stephen Montgomery, Obi Griffith, \ and Steven Jones from Canada's Michael Smith Genome Sciences Centre, Vancouver, \ British Columbia, Canada.
\\ The ORegAnno community (please see individual citations for various\ features): ORegAnno Citation.\ \
\
Lesurf R, Cotto KC, Wang G, Griffith M, Kasaian K, Jones SJ, Montgomery SB, Griffith OL, Open\
Regulatory Annotation Consortium..\
\
ORegAnno 3.0: a community-driven resource for curated regulatory annotation.\
Nucleic Acids Res. 2016 Jan 4;44(D1):D126-32.\
PMID: 26578589; PMC:
\
Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M,\
Haeussler M et al.\
\
ORegAnno: an open-access community-driven resource for regulatory annotation.\
Nucleic Acids Res. 2008 Jan;36(Database issue):D107-13.\
PMID: 18006570; PMC:
\ Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, \ Prychyna Y, Zhang X, Jones SJ. \ ORegAnno: an open access database and curation system for \ literature-derived promoters, transcription factor binding sites and regulatory variation.\ Bioinformatics. 2006 Mar 1;22(5):637-40.\ PMID: 16397004\
\ \ regulation 1 color 102,102,0\ group regulation\ longLabel Regulatory elements from ORegAnno\ shortLabel ORegAnno\ track oreganno\ type bed 4 +\ visibility hide\ xenoMrna Other mRNAs psl xeno Non-D. melanogaster mRNAs from GenBank 0 100 0 0 0 127 127 127 1 0 0\ This track displays translated blat alignments of vertebrate and\ invertebrate mRNA in \ GenBank from organisms other than D. melanogaster.\ \
\ 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, click \ here.\
\ \\ The mRNAs were aligned against the D. melanogaster 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 D. melanogaster, 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 D. melanogaster 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:
This track is based on text-mining of full-text biomedical articles and includes two types of subtracks:
\ \Both sources of information are linked to the respective articles.\
Background information on how permission to full-text data was obtained can be found on the The sequence subtrack indicates the location of sequences in publications\
mapped back to the genome, annotated with the first author and the year of the\
publication. All matches of one article are grouped ("chained") together.\
Article titles are shown when you move the mouse cursor over the features.\
Thicker parts of the features (exons) represent matching sequences,\
connected by thin lines to matches from the same article within 30 kbp. The subtrack "individual sequence matches" activates automatically when\
the user clicks a sequence match and follows the link "Show sequence matches individually" \
from the details page. Mouse-overs show flanking text around the sequence, and clicking\
features links to BLAT alignments.\
All other subtracks (i.e. bands, genes, SNPs) show the number of matching articles as\
the feature description. Clicking on them shows the sentences and sections in articles \
where the identifiers were found. The track configuration includes a keyword and year filter. Keywords are space-separated\
and are searched in the article's title, author list, and abstract. The track is based on text from biomedical research articles, obtained as\
part of the UCSC Genocoding Project. The current dataset consists of about 600,000 files (main text and\
supplementary files) from PubMed Central (Open-Access set) and around 6 million text\
files (main text) from Elsevier (as part of the \
All file types (including XML, raw ASCII, PDFs and various Microsoft\
Office formats (Excel, Word, PowerPoint)) were converted to text. The results were processed \
to find groups of words that look like DNA/RNA sequences or\
words that look like protein sequences. These were then mapped with BLAT to the\
human genome and these model organisms: mouse (mm9), rat (rn4), zebrafish\
(danRer6), Drosophila melanogaster (dm3), X. tropicalis (xenTro2), Medaka\
(oryLat2), C. intestinalis (ci2), C. elegans (ce6) and yeast (sacCer2).\
\
The pipeline roughly proceeds through these steps:\
Note that due to the 90% identity filter, some sequences do not match\
anywhere in the genome. Examples include primers with added restriction sites,\
mutation primers, or any other sequence that joins or mixes two pieces of genomic\
DNA not part of RefSeq. Also note that some gene symbols correspond to \
English words which can sometimes lead to many false positives. Software and processing by Maximilian Haeussler. UCSC Track visualisation by\
Larry Meyer and Hiram Clawson. Elsevier support by Max Berenstein, Raphael\
Sidi, Judd Dunham, Scott Robbins and colleagues. Original version written at the Display Convention and Configuration
\
Data
\
Methods
\
\
\
\
Credits
\
Feedback
\
Please send ideas, comments or feedback on this track to\
\
max@soe.ucsc.edu.\
\
We are very interested in getting access to more articles from publishers for this\
dataset; see the project website.\
\
Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM,\
Open Regulatory Annotation Consortium.\
\
Text-mining assisted regulatory annotation.\
Genome Biol. 2008;9(2):R31.\
PMID: 18271954; PMC:
\
Haeussler M, Gerner M, Bergman CM.\
\
Annotating genes and genomes with DNA sequences extracted from biomedical articles.\
Bioinformatics. 2011 Apr 1;27(7):980-6.\
PMID: 21325301; PMC:
\ Van Noorden R.\ \ Trouble at the text mine.\ Nature. 2012 Mar 7;483(7388):134-5.\
\ pub 1 color 0,0,0\ compositeTrack on\ group pub\ longLabel Publications: Sequences in Scientific Articles\ nextExonText Next Match\ noInherit on\ prevExonText Prev Match\ pubsArticleTable hgFixed.pubsArticle\ pubsMarkerTable hgFixed.pubsMarkerAnnot\ pubsPslTrack pubsBlatPsl\ pubsSequenceTable hgFixed.pubsSequenceAnnot\ shortLabel Publications\ track pubs\ type bed 4\ visibility dense\ 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 is powered by Bing! and Microsoft Research. UCSC collaborators at\ Microsoft Research (Bob Davidson, David Heckerman) implemented a DNA sequence\ detector and processed thirty days of web crawler updates, which covers\ roughly 40 billion webpages. The results were mapped with BLAT to the genome.
\ \The track indicates the location of sequences on web pages\ mapped to the genome, labelled with the web page URL. If the web page includes\ invisible meta data, then the first author and a year of publication \ is shown instead of the URL. All\ matches of one web page are grouped ("chained") together.\ Web page titles are shown when you move the mouse cursor over the features.\ Thicker parts of the features (exons) represent matching sequences,\ connected by thin lines to matches from the same web page within 30 kbp.
\ \ \ \\ All file types (PDFs and various Microsoft Office formats) were converted to\ text. The results were processed to find groups of words that look like DNA/RNA\ sequences. These were then mapped with BLAT to the human genome using the same\ software as used in the Publication track.
\ \DNA sequence detection by Bob Davidson at Microsoft Research. \ HTML parsing and sequence mapping by Maximilian Haeussler at UCSC.
\ \\
Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM, Open Regulatory Annotation Consortium.\
\
Text-mining assisted regulatory annotation.\
Genome Biol. 2008;9(2):R31.\
PMID: 18271954; PMC:
\
Haeussler M, Gerner M, Bergman CM.\
\
Annotating genes and genomes with DNA sequences extracted from biomedical articles.\
Bioinformatics. 2011 Apr 1;27(7):980-6.\
PMID: 21325301; PMC:
\ Van Noorden R.\ \ Trouble at the text mine.\ Nature. 2012 Mar 7;483(7388):134-5.\
\ pub 1 configurable off\ configureByPopup off\ group pub\ longLabel DNA Sequences in Web Pages Indexed by Bing.com / Microsoft Research\ nextExonText Next Match\ prevExonText Prev Match\ pubsArticleTable hgFixed.pubsBingArticle\ pubsMarkerTable hgFixed.pubsBingMarkerAnnot\ pubsPslTrack pubsBingBlatPsl\ pubsSequenceTable hgFixed.pubsBingSequenceAnnot\ shortLabel Web Sequences\ track pubsBingBlat\ type bed 12 +\ visibility hide\ cons15way Conservation (15) bed 4 12 Flies, Mosquito, Honeybee, Beetle Multiz Alignments & phastCons Scores 2 104.2 0 0 0 127 127 127 0 0 0\ This track shows a measure of evolutionary conservation in \ twelve Drosophila species, mosquito, honeybee and red flour beetle,\ based on a phylogenetic hidden Markov model (phastCons).\ Multiz alignments of the following assemblies were used to generate this\ annotation: \
\ In full and pack display modes, conservation scores are displayed as\ a "wiggle" (histogram), where the height reflects the \ size of the score. Pairwise alignments of each \ species to the D. melanogaster genome are displayed below 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.
\\ The conservation wiggle 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.
\\ Checkboxes in the track configuration section allow excluding\ species from the pairwise display; however, this does not remove them\ from the conservation score display.\ To view detailed information about the alignments at a specific\ position, zoom in the display 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 D. melanogaster sequence at those \ alignment positions relative to the longest non-D. melanogaster sequence. \ If there is sufficient space in the display, the size of the gap is shown; \ if not, and if the gap size is a multiple of 3, a "*" is displayed, \ otherwise "+" is shown.
\\ 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:\ \
\ \ \\
\ Gene Track Species \ FlyBase Genes D. melanogaster \ mRNAs D. simulans, D. yakuba,\ A. gambiae, A. mellifera \ not translated All other species
\ Best-in-genome pairwise alignments were generated for each species \ using blastz, followed by chaining and netting. The pairwise alignments\ were then multiply aligned using the multiz program, \ according to this topology:\
\
(((((((((dm3 (droSim1 droSec1))\
(droYak2 droEre2)) droAna3)\
(dp4 droPer1)) droWil1)\
((droVir3 droMoj3) droGri2))\
anoGam1) apiMel3) triCas2)\
\
The resulting multiple alignments were then assigned \
conservation scores by phastCons.\
The phastCons parameters for the 15-way Drosophila annotations are: \ expected-length = 23.8; target-coverage = 0.393; rho is set to the \ default value = 0.3.
\\ 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. Note that, unlike many\ conservation-scoring programs, phastCons does not rely on a sliding window\ of fixed size, so 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).
\\ PhastCons currently treats alignment gaps as missing data, which\ sometimes has the effect of producing undesirably high conservation scores\ in gappy regions of the alignment. We are looking at several possible ways\ of improving the handling of alignment gaps.
\ \This track was created at UCSC using the following programs:\
\ 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\
\ \\
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\
\ \\
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 alignments of A. gambiae (anoGam1, Feb. 2003 (IAGEC MOZ2/anoGam1)) to the\ D. melanogaster genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ A. gambiae and D. melanogaster simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. The A. gambiae sequence is \ from the \ MOZ2 assembly.
\\ 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\ A. gambiae assembly or an insertion in the D. melanogaster \ 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 D. melanogaster 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 A. gambiae/D. melanogaster genomes were aligned with \ blastz and converted into axt format using the lavToAxt program.\ The axt alignments were fed into axtChain, which organizes all \ alignments between a single A. gambiae chromosome and a single \ D. melanogaster 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 were discarded; the remaining \ chains are displayed in this track.\ \\
\ A C G T \ A 91 -90 -25 -100 \ C -90 100 -100 -25 \ G -25 -100 100 -90 \ T -100 -25 -90 91
\ 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 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 A. gambiae/D. melanogaster chain for \ every part of the D. melanogaster genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The A. gambiae sequence used in this annotation is \ from the Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1) 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.
\\ Lineage-specific repeats were identified by Arian Smit and his program \ RepeatMasker.
\\ 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 RC,\
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 D. pseudoobscura (dp3, Nov. 2004 (FlyBase 1.03/dp3)) to the\ D. melanogaster genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ D. pseudoobscura and D. melanogaster 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\ D. pseudoobscura assembly or an insertion in the D. melanogaster \ 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 D. melanogaster 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 D. pseudoobscura/D. melanogaster genomes were aligned with \ blastz and converted into axt format using the lavToAxt program.\ The axt alignments were fed into axtChain, which organizes all \ alignments between a single D. pseudoobscura chromosome and a single \ D. melanogaster 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 were discarded; the remaining \ chains are displayed in this track.\ \\
\ A C G T \ A 91 -90 -25 -100 \ C -90 100 -100 -25 \ G -25 -100 100 -90 \ T -100 -25 -90 91
\ 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 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 D. pseudoobscura/D. melanogaster chain for \ every part of the D. melanogaster genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The D. pseudoobscura sequence used in this annotation is \ from the Nov. 2004 (FlyBase 1.03/dp3) (dp3) 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 dp3 data were obtained from the FlyBase Release 1.0 assembly.
\\ 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.
\\ Lineage-specific repeats were identified by Arian Smit and his program \ RepeatMasker.
\\ 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 RC,\
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 D. persimilis (droPer1, Oct. 2005 (Broad/droPer1)) to the\ D. melanogaster genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ D. persimilis and D. melanogaster 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\ D. persimilis assembly or an insertion in the D. melanogaster \ 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 D. melanogaster 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 D. persimilis/D. melanogaster genomes were aligned with \ blastz and converted into axt format using the lavToAxt program.\ The axt alignments were fed into axtChain, which organizes all \ alignments between a single D. persimilis chromosome and a single \ D. melanogaster 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 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 D. persimilis/D. melanogaster chain for \ every part of the D. melanogaster genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The D. persimilis sequence used in this annotation is \ from the Oct. 2005 (Broad/droPer1) (droPer1) 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.
\\ Lineage-specific repeats were identified by Arian Smit and his program \ RepeatMasker.
\\ 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 RC,\
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 D. ananassae (droAna2, Aug. 2005 (Agencourt prelim/droAna2)) to the\ D. melanogaster genome using a gap scoring system that allows longer gaps than \ traditional affine gap scoring systems. It can also tolerate gaps in both \ D. ananassae and D. melanogaster 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 \ D. ananassae assembly or an insertion in the D. melanogaster 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 D. melanogaster 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 D. ananassae/D. melanogaster\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz, and the transposons were then 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 D. ananassae chromosome and a single\ D. melanogaster 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 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 D. ananassae/D. melanogaster chain for \ every part of the D. melanogaster genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The D. ananassae sequence used in this annotation is from\ the Aug. 2005 (Agencourt prelim/droAna2) (droAna2) 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.
\ \\
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 shows alignments of D. erecta (droEre1, Aug. 2005 (Agencourt prelim/droEre1)) to the\ D. melanogaster genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ D. erecta and D. melanogaster 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\ D. erecta assembly or an insertion in the D. melanogaster \ 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 D. melanogaster 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 D. erecta/D. melanogaster genomes were aligned with \ blastz and converted into axt format using the lavToAxt program.\ The axt alignments were fed into axtChain, which organizes all \ alignments between a single D. erecta chromosome and a single \ D. melanogaster 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 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 D. erecta/D. melanogaster chain for \ every part of the D. melanogaster genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The D. erecta sequence used in this annotation is \ from the Aug. 2005 (Agencourt prelim/droEre1) (droEre1) 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.
\\ Lineage-specific repeats were identified by Arian Smit and his program \ RepeatMasker.
\\ 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 RC,\
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 D. yakuba (droYak2, Nov. 2005 (WUGSC 7.1/droYak2)) to the\ D. melanogaster genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ D. yakuba and D. melanogaster 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\ D. yakuba assembly or an insertion in the D. melanogaster \ 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 D. melanogaster 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 D. yakuba/D. melanogaster genomes were aligned with \ blastz and converted into axt format using the lavToAxt program.\ The axt alignments were fed into axtChain, which organizes all \ alignments between a single D. yakuba chromosome and a single \ D. melanogaster 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 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 D. yakuba/D. melanogaster chain for \ every part of the D. melanogaster genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The D. yakuba sequence used in this annotation is from\ the Nov. 2005 (WUGSC 7.1/droYak2) (droYak2) 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.
\ \\
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 shows alignments of D. sechellia (droSec1, Oct. 2005 (Broad/droSec1)) to the\ D. melanogaster genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ D. sechellia and D. melanogaster 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\ D. sechellia assembly or an insertion in the D. melanogaster \ 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 D. melanogaster 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 D. sechellia/D. melanogaster genomes were aligned with \ blastz and converted into axt format using the lavToAxt program.\ The axt alignments were fed into axtChain, which organizes all \ alignments between a single D. sechellia chromosome and a single \ D. melanogaster 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 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 D. sechellia/D. melanogaster chain for \ every part of the D. melanogaster genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The D. sechellia sequence used in this annotation is \ from the Oct. 2005 (Broad/droSec1) (droSec1) 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.
\\ Lineage-specific repeats were identified by Arian Smit and his program \ RepeatMasker.
\\ 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 RC,\
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 D. simulans (droSim1, Apr. 2005 (WUGSC mosaic 1.0/droSim1)) to the\ D. melanogaster genome using a gap scoring system that allows longer gaps than \ traditional affine gap scoring systems. It can also tolerate gaps in both \ D. simulans and D. melanogaster 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 \ D. simulans assembly or an insertion in the D. melanogaster 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 D. melanogaster 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 blastz alignments were converted into axt format using the lavToAxt\ program. The axt alignments were fed into axtChain, which organizes all \ alignments between a single D. simulans chromosome and a single\ D. melanogaster 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 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 D. simulans/D. melanogaster chain for \ every part of the D. melanogaster genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The D. simulans sequence used in this annotation is from\ the Apr. 2005 (WUGSC mosaic 1.0/droSim1) (droSim1) 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.
\ \\
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 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 and GIRI\ for providing the tools and repeat libraries used to generate this track.
\ \\ Jurka J.\ Repbase update: a database and an electronic journal of repetitive elements.\ Trends Genet. 2000 Sep;16(9):418-20.\ PMID: 10973072\
\ varRep 0 canPack off\ group varRep\ longLabel Repeating Elements by RepeatMasker\ priority 149.1\ shortLabel RepeatMasker\ spectrum on\ track rmsk\ type rmsk\ visibility dense\