This track shows the draft assembly of the $organism genome.\ This assembly merges contigs from overlapping drafts and\ finished clones into longer sequence contigs. The sequence\ contigs are ordered and oriented when possible by mRNA, EST,\ paired plasmid reads (from the SNP Consortium) and BAC end\ sequence pairs.
\In dense mode, this track depicts the path through the draft and \ finished clones (aka the golden path) used to create the assembled sequence. \ Clone boundaries are distinguished by the use of alternating gold and brown \ coloration. Where gaps\ exist in the path, spaces are shown between the gold and brown\ blocks. If the relative order and orientation of the contigs\ between the two blocks is known, a line is drawn to bridge the\ blocks.
\\ Clone Type Key:\
\ There are no gaps in the WS100 $organism assembly. \ Instead, this track shows the few remaining unknown bases.\ The bases are distibuted across the genome as follows:\
\ The GC percent track shows the percentage of G (guanine) and C (cytosine) bases\ in a 20,000 base window. Windows with high GC content are drawn more darkly \ than windows with low GC content. High GC content is typically associated with \ gene-rich areas.\
\\ This track was generated at UCSC.\ map 1 refGene RefSeq Genes genePred refPep refMrna RefSeq Genes 3 35 12 12 120 133 133 187 0 0 0
\ The RefSeq Genes track shows known protein-coding genes taken from \ the NCBI mRNA reference sequences collection (RefSeq). On assemblies in \ which incremental GenBank downloads are supported, the data underlying this \ track are updated nightly.
\ \\ 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. \
\ After you have made your selections, click the Submit button to \ return to the tracks display page.
\ \\ RefSeq mRNAs were aligned against the $Organism genome using blat; \ those with an alignment of less than 15% were discarded. When a single mRNA \ 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 mRNA 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.
\ \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.\
\ genes 1 idXref refLink mrnaAcc name\ twinscan Twinscan genePred twinscanPep Twinscan Gene Predictions Using briggsae/elegans Homology 0 45 0 100 100 127 177 177 0 0 0\ The Twinscan program predicts genes in a manner similar to Genscan, except \ that Twinscan takes advantage of genome comparisons to improve gene prediction\ accuracy. More information and a web server can be found at\ http://mblab.wustl.edu/.
\ \\ This track follows the display conventions for \ gene prediction \ tracks.
\\ The track description page offers the following filter and configuration\ options:\
\ The Twinscan algorithm is described in Korf, I. et al. (2001) in the\ References section below.
\ \\ Thanks to Michael Brent's Computational Genomics Group at Washington \ University St. Louis for providing these data.
\ \\ Korf I, Flicek P, Duan D, Brent MR.\ Integrating genomic homology into gene structure prediction.\ Bioinformatics. 2001 Jun 1;17(90001)S140-8.
\ genes 1 sangerGene WormBase Genes genePred sangerPep WormBase Gene Annotations 3 48 0 0 200 127 127 227 0 0 6 chrI,chrII,chrIII,chrIV,chrV,chrX, http://www.wormbase.org/db/gene/gene?name=$$\ NOTE: These annotations appear only on chromosomes I, II, III, IV, V, and X.\ \
The Sanger gene predictions are produced by \ WormBase. Thanks to\ the WormBase Consortium for providing these data.\ genes 1 directUrl /cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s\ hgGene on\ hgsid on\ softberryGene Fgenesh++ Genes genePred softberryPep Fgenesh++ Gene Predictions 1 48 0 100 0 127 177 127 0 0 0
\ Gene predictions on $date release of $organism sequences.\ Fgenesh++ predictions are based on Softberry's gene finding software. \ The set of 19112 genes includes 4682 genes corresponding to known mRNAs, \ 13085 having similarity with proteins from NR database, and \ 1345 ab initio predictions.
\ \\ Fgenesh++ uses both hidden Markov models (HMMs) and \ protein similarity to find genes in a completely automated manner. For more \ information, see Solovyev, V.V. (2001) in the References section below.
\ \\ The Fgenesh++ gene predictions were produced by \ Softberry Inc. \ Commercial use of these predictions is restricted to viewing in \ this browser. Please contact Softberry Inc. to make arrangements for further \ commercial access.
\ \\ Solovyev, V.V. \ "Statistical approaches in Eukaryotic gene prediction" in the \ Handbook of Statistical Genetics (ed. Balding, D. et al.), \ 83-127. John Wiley & Sons, Ltd. (2001).
\ genes 1 mrna $Organism mRNAs psl . $Organism mRNAs from GenBank 3 54 0 0 0 127 127 127 1 0 0\ The mRNA track shows alignments between $Organism 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 $Organism 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.
\\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ rna 1 baseColorDefault diffCodons\ baseColorUseCds genbank\ baseColorUseSequence genbank\ indelDoubleInsert on\ indelPolyA on\ indelQueryInsert on\ showDiffBasesAllScales .\ est $Organism ESTs psl est $Organism ESTs Including Unspliced 0 57 0 0 0 127 127 127 1 0 0\ This track shows alignments between $Organism 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, $Organism ESTs from GenBank were aligned \ against the genome using blat. Note that the maximum intron length\ allowed by blat is 750,000 bases, which may eliminate some ESTs with very \ long introns that might otherwise align. When a single \ EST aligned in multiple places, the alignment having the \ highest base identity was identified. Only alignments having\ a base identity level within 0.5% of the best and at least 96% base identity \ with the genomic sequence were kept.
\ \\ This track was produced at UCSC from EST sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J,\ Wheeler DL.\ GenBank: update. Nucleic Acids Res.\ 2004 Jan 1;32(Database issue):D23-6.
\\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ rna 1 baseColorUseSequence genbank\ indelDoubleInsert on\ indelQueryInsert on\ intronGap 30\ miRNA miRNA bed 8 . MicroRNAs from miRBase 0 63 255 64 64 255 159 159 1 0 0 http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$$\ The miRNA track shows microRNAs from the\ \ miRBase at The \ Wellcome Trust Sanger Institute.
\ \\ Mature miRNAs (miRs) are represented by \ thick blocks. The predicted stem-loop portions of the primary transcripts\ are indicated by thinner blocks. miRNAs in the sense orientation are shown in\ black; those in the reverse orientation are colored grey. When a single \ precursor produces two mature miRs from its 5' and 3' parts, it is displayed \ twice with the two different positions of the mature miR.
\\ To display only those items that exceed a specific unnormalized score, enter\ a minimum score between 0 and 1000 in the text box at the top of the track \ description page.\
\ \\ Mature and precursor miRNAs from the miRNA Registry were\ aligned against the genome using blat.\ The extents of the precursor sequences were not generally known, and were\ predicted based on base-paired hairpin structure. \ miRBase is described in Griffiths-Jones, S. et al. (2006).\ The miRNA Registry is\ described in Griffiths-Jones, S. (2004) and Weber, M.J. (2005) in the \ References section below.
\ \\
\
This track was created by Michel Weber of
\ When making use of these data, please cite:
\\ Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ.\ miRBase: microRNA sequences, targets and gene nomenclature.\ Nucleic Acids Res. 2006 Jan 1;34(Database issue):D140-4.
\\ Griffiths-Jones S. \ The microRNA Registry.\ Nucleic Acids Res. 2004 Jan 1;32(Database issue):D109-11.
\\ Weber MJ. \ New human and mouse microRNA genes found by homology search.\ Febs J. 2005 Jan;272(1):59-73.
\\ You may also want to cite The Wellcome Trust Sanger Institute \ miRNA Registry.
\\
The following publication provides guidelines on miRNA annotation:\
Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X,\
Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M et al.\
A uniform system for microRNA annotation. \
RNA. 2003 Mar;9(3):277-9.
\
For more information on blat, see \
Kent WJ.\
BLAT - the BLAST-like alignment tool.\
Genome Res. 2002 Apr;12(4):656-64.
\ This track displays alignments of $o_organism to $organism \ using the Wobble Aware Bulk Aligner (WABA), an alignment tool developed by Jim\ Kent for doing large-scale alignments between genomic DNA of different \ species.
\\ The symbols shown below the base alignments on the details page indicate the \ hidden Markov model states for those bases:\
\ The WABA alignment algorithm is described in Kent, W.J. and Zahler, A.M. \ Conservation, regulation, synteny, and introns in a large-scale\ C. briggsae-C. elegans genomic alignment.\ Genome Res 10(8), 1115-1125 (2000).
\ \\ WABA was developed by \ Jim Kent and\ Alan M. Zahler.\
\\ $o_Organism\ version cb25.agp8 (11 July 2002) and $organism \ version WS100 (02 May 2003) were used in creating this \ annotation. Thanks to \ WormBase\ and Lincoln Stein.\
\\ The data for the $organism browser display were collected by \ Hiram Clawson. \ Please contact him with questions or comments about this annotation.\
\ compGeno 0 otherDb cb1\ cb1Chain Briggsae Chain chain cb1 $o_Organism ($o_date/$o_db) Chained Alignments 0 125 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_Organism ($o_db, $o_date) to the\ $Organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_Organism and $Organism 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\ $o_Organism assembly or an insertion in the $Organism \ 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 $Organism 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.
\ \\ Transposons that have been inserted since the \ $o_Organism/$Organism\ 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 $o_Organism chromosome and a single\ $Organism 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, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., \ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ. \ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 1 otherDb cb1\ genomicSuperDups Segmental Dups bed 6 . Duplications of >1000 Bases of Non-RepeatMasked Sequence 0 146 0 0 0 127 127 127 0 0 0\ This track shows regions detected as putative genomic duplications within the\ golden path. The following display conventions are used to distinguish\ levels of similarity:\
\ Segmental duplications play an important role in both genomic disease \ and gene evolution. This track displays an analysis of the global \ organization of these long-range segments of identity in genomic sequence.\
\ \Large recent duplications (>= 1 kb and >= 90% identity) were detected\ by identifying high-copy repeats, removing these repeats from the genomic \ sequence ("fuguization") and searching all sequence for similarity. The \ repeats were then reinserted into the pairwise alignments, the ends of \ alignments trimmed, and global alignments were generated.\ For a full description of the "fuguization" detection method, see Bailey \ et al. (2001) in the References section below.\ \
\ These data were provided by \ Ginger Cheng, \ Xinwei She \ and Evan Eichler \ at the University of Washington.
\ \\ Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE.\ Segmental duplications: organization and impact within the \ current human genome project assembly.\ Genome Res. 2001 Jun;11(6):1005-17.
\ varRep 1 noScoreFilter .\ rmsk RepeatMasker rmsk Repeating Elements by RepeatMasker 1 149.1 0 0 0 127 127 127 1 0 0\
This track was created by using Arian Smit's
\ In full display mode, this track displays up to ten different classes of repeats:\
\ The level of color shading in the graphical display reflects the amount of \ base mismatch, base deletion, and base insertion associated with a repeat \ element. The higher the combined number of these, the lighter the shading.
\ \\ UCSC has used the most current versions of the RepeatMasker software \ and repeat libraries available to generate these data. Note that these \ versions may be newer than those that are publicly available on the Internet. \
\\ Data are generated using the RepeatMasker -s flag. Additional flags\ may be used for certain organisms. Repeats are soft-masked. Alignments may \ extend through repeats, but are not permitted to initiate in them. \ See the \ FAQ for \ more information.
\ \\ Thanks to Arian Smit and GIRI\ for providing the tools and repeat libraries used to generate this track.
\ \\ RepBase is described in\ Jurka J.\ Repbase update: a database and an electronic journal of\ repetitive elements.\ Trends Genet. 2000 Sep;16(9):418-420.
\ varRep 0 simpleRepeat Simple Repeats bed 4 + Simple Tandem Repeats by TRF 0 149.3 0 0 0 127 127 127 0 0 0\ This track displays simple tandem repeats (possibly imperfect) 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.
\ varRep 1 blatFugu Fugu Blat psl xeno Takifugu rubripes Translated Blat Alignments 0 150 0 60 120 200 220 255 1 0 0\ The Fugu v.3.0 whole genome shotgun assembly was provided by the\ US DOE Joint \ Genome Institute (JGI). The assembly was constructed with the JGI\ assembler, JAZZ, from paired end sequencing reads produced at JGI, Myriad \ Genetics, and Celera Genomics, resulting in a sequence coverage of 5.7X. All \ reads are plasmid, cosmid, or BAC end-sequences, with the predominant coverage\ derived from 2 Kb insert plasmids. This assembly contains 20,379\ scaffolds totaling 319 million base pairs. The largest 679 scaffolds\ total 160 million base pairs.
\\ The strand information (+/-) for this track is in two parts. The\ first + or - indicates the orientation of the query sequence whose\ translated protein produced the match. 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 alignments were made with blat in translated protein mode requiring two\ nearby 4-mer matches to trigger a detailed alignment. The $organism\ genome was masked with RepeatMasker and Tandem Repeat Finder before \ running blat.
\ \\ The 3.0 draft from the\ \ JGI Fugu rubripes website was used in the\ UCSC Genome Browser Fugu blat alignments. These data were freely provided \ by the JGI for use in this publication only.
\ \\ Kent, W.J.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 12(4), 656-664 (2002).
\ \ compGeno 1 blastzCb1 Briggsae Blastz psl xeno cb1 $o_Organism ($o_date/$o_db) Blastz 0 159 0 0 0 50 128 50 1 0 0\ This track displays blastz alignments of the $o_organism assembly ($o_db,\ $o_date) to the $organism genome. The track has an optional \ feature that color codes alignments to indicate the chromosomes from which \ they are derived in the aligning assembly. To activate the color feature, \ click the on button next to "Color track based on\ chromosome" on the track description page.
\ \\ This track has a filter that can be used to change the display mode,\ turn on the chromosome color track, or filter the display output by\ chromosome. The filter is located at the top of the track description page,\ which 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.\
\ When you have finished configuring the filter, click the Submit\ button.
\ \\ These alignments were contributed by Scott Schwartz of the\ Penn State Bioinformatics\ Group. The best-in-genome filtering was done using UCSC's\ axtBest program.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W.\ Scoring pairwise genomic sequence alignments.\ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-mouse alignments with BLASTZ.\ Genome Res. 13(1), 103-107 (2003).
\ compGeno 1 otherDb cb1\ blastzSelf Self Blastz psl xeno ce1 $Organism Blastz Self Alignments 0 159 0 0 0 50 128 50 1 0 0\ This track displays blastz alignments of the $organism assembly to itself.\ The track has an optional feature that color codes alignments to indicate \ the chromosomes from which they are derived in the aligning assembly. To \ activate the color feature, click the on button next to \ "Color track based on chromosome" on the track description page.
\ \\ This track has a filter that can be used to change the display mode,\ turn on the chromosome color track, or filter the display output by\ chromosome. The filter is located at the top of the track description page,\ which 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.\
\ When you have finished configuring the filter, click the Submit\ button.
\ \\ These alignments were contributed by Scott Schwartz of the\ Penn State Bioinformatics\ Group. The best-in-genome filtering was done using UCSC's\ axtBest program.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W.\ Scoring pairwise genomic sequence alignments.\ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-mouse alignments with BLASTZ.\ Genome Res. 13(1), 103-107 (2003).
\ varRep 1 otherDb ce1\ chainSelf Self Chain chain ce1 $Organism Chained Self Alignments 0 400 100 50 0 255 240 200 1 0 0\ This track shows alignments of the $Organism genome with itself, \ using a gap scoring system that allows longer gaps than traditional\ affine gap scoring systems. The system can also tolerate gaps\ in both sets of sequence simultaneously. After filtering out the \ "trivial" alignments produced when identical locations of the \ genome map to one another (e.g. chrN mapping to chrN), \ the remaining alignments point out areas of duplication within the \ $Organism genome.
\\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions. Single lines indicate \ gaps that are largely due to a deletion in the query assembly or an \ insertion in the target assembly. Double lines represent more complex gaps \ that involve substantial sequence in both the query and target assemblies. \ This may result from inversions, overlapping deletions, an abundance of local \ mutation, or an unsequenced gap in one of the assemblies. In cases where \ multiple chains align over a particular region of the $Organism \ genome, the chains with single-lined gaps are often due to processed \ pseudogenes, while chains with double-lined gaps are more often due to \ paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \\ The genome was aligned to itself using blastz. Trivial alignments were \ filtered out, and the remaining alignments were converted into axt format\ using the lavToAxt program. The axt alignments were fed into axtChain, which \ organizes all alignments between a single target chromosome and a single\ query chromosome into a group and creates a kd-tree out of the gapless \ subsections (blocks) of the alignments. A dynamic program was then run over \ the kd-trees to find the maximally scoring chains of these blocks. Chains \ scoring below a threshold were discarded; the remaining chains are displayed \ in this track.
\ \\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his\ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California\ at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.\
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W.\ Scoring pairwise genomic sequence alignments.\ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 13(1), 103-7 (2003).
\ \ varRep 1 otherDb ce1\