\ This track shows the draft assembly of the $organism 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.
\\ 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 "W": \ Whole Genome Shotgun contig.
\ \ map 1 gap Gap bed 3 + Gap Locations 1 11 0 0 0 127 127 127 0 0 0\ This track shows the position of gaps — represented by Ns — within \ the B. taurus assembly. \ All gaps are bridged fragment gaps within the scaffold.\
\ map 1 gc5Base GC Percent wig 0 100 GC Percent in 5-Base Windows 0 23.5 0 0 0 128 128 128 0 0 0\ This track may be configured in a variety of ways to highlight different aspects \ of the displayed information. Click the "Graph configuration help" link\ for an explanation of the configuration options.\ \
The data and presentation of this graph were prepared by\ Hiram Clawson.\ \ map 0 autoScaleDefault Off\ defaultViewLimits 30:70\ graphTypeDefault Bar\ gridDefault OFF\ maxHeightPixels 128:36:16\ spanList 5\ windowingFunction Mean\ quality Quality Scores wig 0 100 $Organism Sequencing Quality Scores 0 23.6 0 128 255 255 128 0 0 0 0
\ The Quality Scores track shows the sequencing quality score \ (range: 0 to 99) of each base in the assembly. \ The height at each position of the track \ indicates the quality of the base. \ When zoomed out to a large range, the heights reflect the averaged scores. \ Scores of 40 or higher reflect high confidence in the sequence (with an error rate of less than \ 1/10,000); scores of 20 or higher reflect reasonable confidence (of working draft \ quality).\
\\ This track may be configured in a variety of ways to highlight different aspects \ of the displayed information. Click the \ Graph \ configuration help link for an explanation of the configuration options.
\ \\ The quality scores were provided as part of the $organism assembly. \ The database representation and graphical display code were written by\ Hiram Clawson.\ map 0 autoScaleDefault Off\ graphTypeDefault Bar\ gridDefault OFF\ maxHeightPixels 128:36:16\ spanList 1,1024\ windowingFunction Mean\ xenoRefGene Other RefSeq genePred xenoRefPep xenoRefMrna Non-$Organism RefSeq Genes 1 35.1 12 12 120 133 133 187 0 0 0
\ This track shows known protein-coding genes from organisms other than \ $organism, taken from the NCBI mRNA reference sequences collection (RefSeq). \
\ \\ 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). \ In some assemblies, non-coding RNA genes are shown in a separate track.
\\ 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 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 0.5% of \ the best and at least 25% 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.
\ genes 1 mgcGenes MGC Genes genePred Mammalian Gene Collection Full ORF mRNAs 3 36 34 139 34 144 197 144 0 0 0\ This track shows alignments of $organism mRNAs from the\ Mammalian Gene Collection \ (MGC) having full-length open reading frames (ORFs) to the genome.
\ \\ The track follows the display conventions for \ gene prediction \ tracks.
\\ An optional codon coloring feature is available for quick\ validation and comparison of gene predictions.\ To display codon colors, select the genomic codons option from the\ Color track by codons pull-down menu. Click \ here for more \ information about this feature.
\ \\ GenBank $organism MGC mRNAs identified as having full-length ORFs \ were aligned against the genome using blat. 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 1% of\ the best and at least 95% base identity with the genomic sequence \ were kept.
\ \\ The $organism MGC full-length mRNA track was produced at UCSC from \ mRNA sequence data submitted to \ GenBank by the \ Mammalian Gene Collection project.
\ \\ Mammalian Gene Collection project references.
\\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ genes 1 geneid Geneid Genes genePred geneidPep Geneid Gene Predictions 0 49 0 90 100 127 172 177 0 0 0\ This track shows gene predictions from the geneid program developed at the \ Genome Bionformatics \ Laboratory (GBL), which is part of the \ Grup de Recerca\ en Informàtica Biomèdica (GRIB) at the Institut Municipal d'Investigació \ Mèdica (IMIM) / Centre de Regulació Genòmica (CRG) in Barcelona."\ \ \
\\ Geneid is a program to predict genes in anonymous genomic sequences designed \ with a hierarchical structure. In the first step, splice sites, start and stop \ codons are predicted and scored along the sequence using Position Weight Arrays \ (PWAs). Next, exons are built from the sites. Exons are scored as the sum of the \ scores of the defining sites, plus the the log-likelihood ratio of a \ Markov Model for coding DNA. Finally, from the set of predicted exons, the gene \ structure is assembled, maximizing the sum of the scores of the assembled exons. \
\\ Thanks to GBL for providing these data.\
\ genes 1 genscan Genscan Genes genePred genscanPep Genscan Gene Predictions 0 50 170 100 0 212 177 127 0 0 0\ This track shows predictions from the \ Genscan program \ written by Chris Burge.\ The predictions are based on transcriptional, \ translational, and donor/acceptor splicing signals, as well as the length \ and compositional distributions of exons, introns and intergenic regions.
\ \\ This track follows the display conventions for \ gene prediction \ tracks. \
\ The track description page offers the following filter and configuration\ options:\
\ For a description of the Genscan program and the model that underlies it, \ refer to Burge and Karlin (1997) in the References section below. \ The splice site models used are described in more detail in Burge (1998)\ below.
\ \\ Burge C. \ Modeling Dependencies in Pre-mRNA Splicing Signals. \ In Salzberg S, Searls D, Kasif S, eds. \ Computational Methods in Molecular Biology, \ Elsevier Science, Amsterdam. 1998;127-163.
\\ Burge C, Karlin S. \ Prediction of Complete Gene Structures in Human Genomic DNA.\ J. Mol. Biol. 1997 Apr 25;268(1):78-94.
\ genes 1 all_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.\ Several types of alignment gap may also be colored; \ for more information, 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.\
\ \\ This 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 .\ intronEst Spliced ESTs psl est $Organism ESTs That Have Been Spliced 1 56 0 0 0 127 127 127 1 0 0\ This track shows alignments between $organism 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. the genomic \ sequence between EST alignment blocks must be at least 32 bases in \ length and have 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 \ $organism 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.\ Several types of alignment gap may also be colored; \ for more information, 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 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.
\\ 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\ maxItems 300\ showDiffBasesAllScales .\ all_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, 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.\ Several types of alignment gap may also be colored; \ for more information, 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 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.
\\ 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\ cpgIslandExt CpG Islands bed 4 + CpG Islands (Islands < 300 Bases are Light Green) 0 90 0 100 0 128 228 128 0 0 0\ CpG islands are associated with genes, particularly housekeeping\ genes, in vertebrates. CpG islands are typically common near\ transcription start sites, and may be associated with promoter\ regions. Normally a C (cytosine) base followed immediately by a \ G (guanine) base (a CpG) is rare in\ vertebrate DNA because the Cs in such an arrangement tend to be\ methylated. This methylation helps distinguish the newly synthesized\ DNA strand from the parent strand, which aids in the final stages of\ DNA proofreading after duplication. However, over evolutionary time\ methylated Cs tend to turn into Ts because of spontaneous\ deamination. The result is that CpGs are relatively rare unless\ there is selective pressure to keep them or a region is not methylated\ for some reason, perhaps having to do with the regulation of gene\ expression. CpG islands are regions where CpGs are present at\ significantly higher levels than is typical for the genome as a whole.\
\ \\ CpG islands were predicted by searching the sequence one base at a\ time, scoring each dinucleotide (+17 for CG and -1 for others) and\ identifying maximally scoring segments. Each segment was then\ evaluated for the following criteria:\
\ The CpG count is the number of CG dinucleotides in the island. \ The Percentage CpG is the ratio of CpG nucleotide bases\ (twice the CpG count) to the length. The ratio of observed to expected \ CpG is calculated according to the formula cited in \ Gardiner-Garden et al. (1987) in the References section below: \
\
Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)\
\
where N = length of sequence.\
\
\
\ This track was generated using a\ modification of a program developed by G. Miklem and L. Hillier.
\ \\ Gardiner-Garden M, Frommer M. \ CpG islands in vertebrate genomes.\ J. Mol. Biol. 1987 Jul 20;196(2):261-82.
\ regulation 1 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.
\ \\ Smit, AFA, Hubley, R and Green, P. RepeatMasker Open-3.0.\ http://www.repeatmasker.org. 1996-2007.\
\\ 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.
\\ For a discussion of repeats in mammalian genomes, see: \
\ Smit AF. Interspersed repeats and other mementos of transposable \ elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6):\ 657-63.
\\ Smit AF. The origin of interspersed repeats in the human genome. \ Curr Opin Genet Dev. 1996 Dec;6(6):743-8.\
\ 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 chainHg17 $o_Organism Chain chain hg17 $o_Organism ($o_date/$o_db) Chained Alignments 0 157 100 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 scaffold, 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 scaffold 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 hg17\ netHg17 $o_Organism Net netAlign hg17 chainHg17 $o_Organism ($o_date/$o_db) Alignment Net 0 157.5 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) 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, 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 0 otherDb hg17\ blastHg17KG Human Proteins psl protein Human (hg17) proteins mapped by chained tBLASTn 3 201 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 hg17 Known Genes track as \ of 08 Dec 2004.\ \
\ 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 required to produce this track\ were written by Jim Kent or Brian Raney.\ genes 1 blastRef hg17.blastKGRef01\ colorChromDefault off\ pred hg17.blastKGPep01\ chainMm6 $o_Organism Chain chain mm6 $o_Organism ($o_date/$o_db) Chained Alignments 0 210 100 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 mm6\ netMm6 $o_Organism Net netAlign mm6 chainMm6 $o_Organism ($o_date/$o_db) Alignment Net 0 210.1 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) 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, 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 0 otherDb mm6\