cb5d901d0f72940e7170a139e44b021121e64412 jnavarr5 Tue Apr 23 09:33:54 2019 -0700 Updating http to https for panTro5, uiLinks cronjob. diff --git src/hg/makeDb/trackDb/transMapTailer.html src/hg/makeDb/trackDb/transMapTailer.html index c83c0d1..abe6adc 100644 --- src/hg/makeDb/trackDb/transMapTailer.html +++ src/hg/makeDb/trackDb/transMapTailer.html @@ -1,136 +1,136 @@ <H2>Display Conventions and Configuration</H2> <P> This track follows the display conventions for <A HREF="../goldenPath/help/hgTracksHelp.html#PSLDisplay" TARGET=_blank>PSL alignment tracks</A>. </P> <P> This track may also be configured to display codon coloring, a feature that allows the user to quickly compare cDNAs against the genomic sequence. For more information about this option, click <A HREF="../goldenPath/help/hgCodonColoringMrna.html" TARGET=_blank>here</A>. Several types of alignment gap may also be colored; for more information, click <A HREF="../goldenPath/help/hgIndelDisplay.html" TARGET=_blank>here</A>. <H2>Methods</H2> <P> <ol> <li> Source transcript alignments were obtained from vertebrate organisms in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes, were used as available. <li> For all vertebrate assemblies that had BLASTZ alignment chains and nets to the $organism ($db) genome, a subset of the alignment chains were selected as follows: <ul> <li> For organisms whose branch distance was no more than 0.5 (as computed by <tt>phyloFit</tt>, see Conservation track description for details), syntenic filtering was used. Reciprocal best nets were used if available; otherwise, nets were selected with the <tt>netfilter -syn</tt> command. The chains corresponding to the selected nets were used for mapping. <li> For more distant species, where the determination of synteny is difficult, the full set of chains was used for mapping. This allows for more genes to map at the expense of some mapping to paralogus regions. The post-alignment filtering step removes some of the duplications. </ul> <li> The <tt>pslMap</tt> program was used to do a base-level projection of the source transcript alignments via the selected chains to the $organism genome, resulting in pairwise alignments of the source transcripts to the genome. <li> The resulting alignments were filtered with <tt>pslCDnaFilter</tt> with a global near-best criteria of 0.5% in finished genomes (human and mouse) and 1.0% in other genomes. Alignments where less than 20% of the transcript mapped were discarded. </ol> </P> <P> To ensure unique identifiers for each alignment, cDNA and gene accessions were made unique by appending a suffix for each location in the source genome and again for each mapped location in the destination genome. The format is: <pre> accession.version-srcUniq.destUniq </pre> Where <tt>srcUniq</tt> is a number added to make each source alignment unique, and <tt>destUniq</tt> is added to give the subsequent TransMap alignments unique identifiers. </P> <P> For example, in the cow genome, there are two alignments of mRNA <tt>BC149621.1</tt>. These are assigned the identifiers <tt>BC149621.1-1</tt> and <tt>BC149621.1-2</tt>. When these are mapped to the human genome, <tt>BC149621.1-1</tt> maps to a single location and is given the identifier <tt>BC149621.1-1.1</tt>. However, <tt>BC149621.1-2</tt> maps to two locations, resulting in <tt>BC149621.1-2.1</tt> and <tt>BC149621.1-2.2</tt>. Note that multiple TransMap mappings are usually the result of tandem duplications, where both chains are identified as syntenic. </P> <h2>Data Access</h2> <p> The raw data for these tracks can be accessed interactively through the <a href="hgTables">Table Browser</a> or the <a href="hgIntegrator">Data Integrator</a>. For automated analysis, the annotations are stored in <a href="../goldenPath/help/bigPsl.html">bigPsl</a> files (containing a number of extra columns) and can be downloaded from our <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/transMap/V4/">download server</a>. The files are associated with these tracks in the following way: <ul> <li>TransMap Ensembl - <tt>$db.ensembl.transMapV4.bigPsl</tt></li> <li>TransMap RefGene - <tt>$db.refseq.transMapV4.bigPsl</tt></li> <li>TransMap RNA - <tt>$db.rna.transMapV4.bigPsl</tt></li> <li>TransMap ESTs - <tt>$db.est.transMapV4.bigPsl</tt></li> </ul> Individual regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt> which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain only features within a given range, for example: <p><tt> bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$db/transMap/V4/$db.refseq.transMapV4.bigPsl -chrom=chr6 -start=0 -end=1000000 stdout </tt> <H2>Credits</H2> <P> This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data submitted to the international public sequence databases by scientists worldwide and annotations produced by the RefSeq, Ensembl, and GENCODE annotations projects.</P> <H2>References</H2> <p> Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C <em>et al</em>. <a href="https://genome.cshlp.org/content/17/12/1763.long" target="_blank"> Targeted discovery of novel human exons by comparative genomics</a>. <em>Genome Res</em>. 2007 Dec;17(12):1763-73. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17989246" target="_blank">17989246</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099585/" target="_blank">PMC2099585</a> </p> <p> Stanke M, Diekhans M, Baertsch R, Haussler D. <a href="https://academic.oup.com/bioinformatics/article/24/5/637/202844/Using-native-and-syntenically-mapped-cDNA" target="_blank"> Using native and syntenically mapped cDNA alignments to improve de novo gene finding</a>. <em>Bioinformatics</em>. 2008 Mar 1;24(5):637-44. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18218656" target="_blank">18218656</a> </p> <p> Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. -<a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030247" +<a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030247" target="_blank"> Comparative genomics search for losses of long-established genes on the human lineage</a>. <em>PLoS Comput Biol</em>. 2007 Dec;3(12):e247. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18085818" target="_blank">18085818</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2134963/" target="_blank">PMC2134963</a> </p>