---------------------------------------------------------------


panPan2.trackDb.html : Differences exist between hgwbeta and hgw2 

(RR fields taken from public MySql server, not individual machine)

2433,2436d2432
< ncbiRefSeqGenomicDiff | html
< ncbiRefSeqGenomicDiff | 
< ncbiRefSeqOther | html
< ncbiRefSeqOther | 

3974,4753d3969
< transMapEnsemblV5 | html
< transMapEnsemblV5 | <H2>Description</H2>
< transMapEnsemblV5 | 
< transMapEnsemblV5 | <P>
< transMapEnsemblV5 | This track contains GENCODE or Ensembl alignments produced by
< transMapEnsemblV5 | the <em>TransMap</em> cross-species alignment algorithm from other vertebrate
< transMapEnsemblV5 | species in the UCSC Genome Browser.  GENCODE is Ensembl for human and mouse,
< transMapEnsemblV5 | for other Ensembl sources, only ones with full gene builds are used.
< transMapEnsemblV5 | Projection Ensembl gene annotations will not be used as sources.
< transMapEnsemblV5 | For closer evolutionary distances, the alignments are created using
< transMapEnsemblV5 | syntenically filtered BLASTZ alignment chains, resulting in a prediction of the
< transMapEnsemblV5 | orthologous genes in bonobo.
< transMapEnsemblV5 | </P>
< transMapEnsemblV5 | 
< transMapEnsemblV5 | 
< transMapEnsemblV5 | <H2>Display Conventions and Configuration</H2>
< transMapEnsemblV5 | 
< transMapEnsemblV5 | <P>
< transMapEnsemblV5 | This track follows the display conventions for 
< transMapEnsemblV5 | <A HREF="../goldenPath/help/hgTracksHelp.html#PSLDisplay" 
< transMapEnsemblV5 | TARGET=_blank>PSL alignment tracks</A>. </P>
< transMapEnsemblV5 | <P>
< transMapEnsemblV5 | This track may also be configured to display codon coloring, a feature that
< transMapEnsemblV5 | allows the user to quickly compare cDNAs against the genomic sequence. For more 
< transMapEnsemblV5 | information about this option, click 
< transMapEnsemblV5 | <A HREF="../goldenPath/help/hgCodonColoringMrna.html" TARGET=_blank>here</A>.
< transMapEnsemblV5 | Several types of alignment gap may also be colored; 
< transMapEnsemblV5 | for more information, click 
< transMapEnsemblV5 | <A HREF="../goldenPath/help/hgIndelDisplay.html" TARGET=_blank>here</A>.
< transMapEnsemblV5 | 
< transMapEnsemblV5 | <H2>Methods</H2>
< transMapEnsemblV5 | 
< transMapEnsemblV5 | <P>
< transMapEnsemblV5 |   <ol>
< transMapEnsemblV5 |     <li> Source transcript alignments were obtained from vertebrate organisms
< transMapEnsemblV5 |     in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank 
< transMapEnsemblV5 |     mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes,
< transMapEnsemblV5 |     were used as available.
< transMapEnsemblV5 |     <li> For all vertebrate assemblies that had BLASTZ alignment chains and
< transMapEnsemblV5 |       nets to the bonobo (panPan2) genome, a subset of the alignment chains were
< transMapEnsemblV5 |       selected as follows:
< transMapEnsemblV5 |       <ul>
< transMapEnsemblV5 |       <li> For organisms whose branch distance was no more than 0.5
< transMapEnsemblV5 |         (as computed by <tt>phyloFit</tt>, see Conservation track description for details),
< transMapEnsemblV5 |         syntenic filtering was used.  Reciprocal best nets were used if available;
< transMapEnsemblV5 |         otherwise, nets were selected with the <tt>netfilter -syn</tt> command.
< transMapEnsemblV5 |         The chains corresponding to the selected nets were used for mapping.
< transMapEnsemblV5 |       <li> For more distant species, where the determination of synteny is difficult,
< transMapEnsemblV5 |         the full set of chains was used for mapping. This allows for more genes to
< transMapEnsemblV5 |         map at the expense of some mapping to paralogous regions.  The
< transMapEnsemblV5 |         post-alignment filtering step removes some of the duplications.
< transMapEnsemblV5 |     </ul>
< transMapEnsemblV5 |     <li> The <tt>pslMap</tt> program was used to do a base-level projection of
< transMapEnsemblV5 |       the source transcript alignments via the selected chains
< transMapEnsemblV5 |       to the bonobo genome, resulting in pairwise alignments of the source transcripts to
< transMapEnsemblV5 |       the genome.
< transMapEnsemblV5 |     <li> The resulting alignments were filtered with <tt>pslCDnaFilter</tt>
< transMapEnsemblV5 |       with a global near-best criteria of 0.5% in finished genomes
< transMapEnsemblV5 |       (human and mouse) and 1.0% in other genomes.  Alignments
< transMapEnsemblV5 |       where less than 20% of the transcript mapped were discarded.
< transMapEnsemblV5 |   </ol>
< transMapEnsemblV5 | </P>
< transMapEnsemblV5 | 
< transMapEnsemblV5 | <P>
< transMapEnsemblV5 | To ensure unique identifiers for each alignment, cDNA and gene accessions were
< transMapEnsemblV5 | made unique by appending a suffix for each location in the source genome and
< transMapEnsemblV5 | again for each mapped location in the destination genome.  The format is:
< transMapEnsemblV5 | <pre>
< transMapEnsemblV5 |    accession.version-srcUniq.destUniq
< transMapEnsemblV5 | </pre>
< transMapEnsemblV5 | 
< transMapEnsemblV5 | Where <tt>srcUniq</tt> is a number added to make each source alignment unique, and
< transMapEnsemblV5 | <tt>destUniq</tt> is added to give the subsequent TransMap alignments unique
< transMapEnsemblV5 | identifiers.
< transMapEnsemblV5 | </P>
< transMapEnsemblV5 | <P>
< transMapEnsemblV5 | For example, in the cow genome, there are two alignments of mRNA <tt>BC149621.1</tt>.
< transMapEnsemblV5 | These are assigned the identifiers <tt>BC149621.1-1</tt> and <tt>BC149621.1-2</tt>.
< transMapEnsemblV5 | When these are mapped to the human genome, <tt>BC149621.1-1</tt> maps to a single
< transMapEnsemblV5 | location and is given the identifier <tt>BC149621.1-1.1</tt>.  However, <tt>BC149621.1-2</tt>
< transMapEnsemblV5 | maps to two locations, resulting in <tt>BC149621.1-2.1</tt> and <tt>BC149621.1-2.2</tt>.  Note
< transMapEnsemblV5 | that multiple TransMap mappings are usually the result of tandem duplications, where both
< transMapEnsemblV5 | chains are identified as syntenic.
< transMapEnsemblV5 | </P>
< transMapEnsemblV5 | 
< transMapEnsemblV5 | <h2>Data Access</h2>
< transMapEnsemblV5 | 
< transMapEnsemblV5 | <p>
< transMapEnsemblV5 | The raw data for these tracks can be accessed interactively through the
< transMapEnsemblV5 | <a href="hgTables">Table Browser</a> or the
< transMapEnsemblV5 | <a href="hgIntegrator">Data Integrator</a>.
< transMapEnsemblV5 | For automated analysis, the annotations are stored in
< transMapEnsemblV5 | <a href="../goldenPath/help/bigPsl.html">bigPsl</a> files (containing a
< transMapEnsemblV5 | number of extra columns) and can be downloaded from our
< transMapEnsemblV5 | <a href="http://hgdownload.soe.ucsc.edu/gbdb/panPan2/transMap/">download server</a>, 
< transMapEnsemblV5 | or queried using our <a href="../goldenPath/help/api.html">API</a>. For more 
< transMapEnsemblV5 | information on accessing track data see our 
< transMapEnsemblV5 | <a href="../FAQ/FAQdownloads.html#download36">Track Data Access FAQ</a>.
< transMapEnsemblV5 | The files are associated with these tracks in the following way:
< transMapEnsemblV5 | <ul>
< transMapEnsemblV5 | <li>TransMap Ensembl - <tt>panPan2.ensembl.transMapV4.bigPsl</tt></li>
< transMapEnsemblV5 | <li>TransMap RefGene - <tt>panPan2.refseq.transMapV4.bigPsl</tt></li>
< transMapEnsemblV5 | <li>TransMap RNA - <tt>panPan2.rna.transMapV4.bigPsl</tt></li>
< transMapEnsemblV5 | <li>TransMap ESTs - <tt>panPan2.est.transMapV4.bigPsl</tt></li>
< transMapEnsemblV5 | </ul>
< transMapEnsemblV5 | Individual regions or the whole genome annotation can be obtained using our tool
< transMapEnsemblV5 | <tt>bigBedToBed</tt> which can be compiled from the source code or downloaded as
< transMapEnsemblV5 | a precompiled binary for your system. Instructions for downloading source code and
< transMapEnsemblV5 | binaries can be found
< transMapEnsemblV5 | <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>.
< transMapEnsemblV5 | The tool can also be used to obtain only features within a given range, for example:
< transMapEnsemblV5 | <p><tt>
< transMapEnsemblV5 | bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/panPan2/transMap/V4/panPan2.refseq.transMapV4.bigPsl
< transMapEnsemblV5 | -chrom=chr6 -start=0 -end=1000000 stdout
< transMapEnsemblV5 | </tt>
< transMapEnsemblV5 | 
< transMapEnsemblV5 | <H2>Credits</H2>
< transMapEnsemblV5 | 
< transMapEnsemblV5 | <P>
< transMapEnsemblV5 | This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data
< transMapEnsemblV5 | submitted to the international public sequence databases by 
< transMapEnsemblV5 | scientists worldwide and annotations produced by the RefSeq,
< transMapEnsemblV5 | Ensembl, and GENCODE annotations projects.</P>
< transMapEnsemblV5 | 
< transMapEnsemblV5 | <H2>References</H2>
< transMapEnsemblV5 | <p>
< transMapEnsemblV5 | Siepel A, Diekhans M, Brejov&#225; B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S,
< transMapEnsemblV5 | Lau C <em>et al</em>.
< transMapEnsemblV5 | <a href="https://genome.cshlp.org/content/17/12/1763.long" target="_blank">
< transMapEnsemblV5 | Targeted discovery of novel human exons by comparative genomics</a>.
< transMapEnsemblV5 | <em>Genome Res</em>. 2007 Dec;17(12):1763-73.
< transMapEnsemblV5 | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17989246" target="_blank">17989246</a>; PMC: <a
< transMapEnsemblV5 | href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099585/" target="_blank">PMC2099585</a>
< transMapEnsemblV5 | </p>
< transMapEnsemblV5 | 
< transMapEnsemblV5 | <p>
< transMapEnsemblV5 | Stanke M, Diekhans M, Baertsch R, Haussler D.
< transMapEnsemblV5 | <a href="https://academic.oup.com/bioinformatics/article/24/5/637/202844/Using-native-and-syntenically-mapped-cDNA"
< transMapEnsemblV5 | target="_blank">
< transMapEnsemblV5 | Using native and syntenically mapped cDNA alignments to improve de novo gene finding</a>.
< transMapEnsemblV5 | <em>Bioinformatics</em>. 2008 Mar 1;24(5):637-44.
< transMapEnsemblV5 | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18218656" target="_blank">18218656</a>
< transMapEnsemblV5 | </p>
< transMapEnsemblV5 | 
< transMapEnsemblV5 | <p>
< transMapEnsemblV5 | Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D.
< transMapEnsemblV5 | <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030247"
< transMapEnsemblV5 | target="_blank">
< transMapEnsemblV5 | Comparative genomics search for losses of long-established genes on the human lineage</a>.
< transMapEnsemblV5 | <em>PLoS Comput Biol</em>. 2007 Dec;3(12):e247.
< transMapEnsemblV5 | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18085818" target="_blank">18085818</a>; PMC: <a
< transMapEnsemblV5 | href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2134963/" target="_blank">PMC2134963</a>
< transMapEnsemblV5 | </p>
< transMapEnsemblV5 | 
< transMapEnsemblV5 | 
< transMapEstV5 | html
< transMapEstV5 | <H2>Description</H2>
< transMapEstV5 | 
< transMapEstV5 | <P>
< transMapEstV5 | This track contains GenBank spliced EST alignments produced by
< transMapEstV5 | the <em>TransMap</em> cross-species alignment algorithm
< transMapEstV5 | from other vertebrate species in the UCSC Genome Browser.
< transMapEstV5 | For closer evolutionary distances, the alignments are created using
< transMapEstV5 | syntenically filtered BLASTZ alignment chains, resulting in a prediction of the
< transMapEstV5 | orthologous genes in bonobo.
< transMapEstV5 | </P>
< transMapEstV5 | 
< transMapEstV5 | 
< transMapEstV5 | <H2>Display Conventions and Configuration</H2>
< transMapEstV5 | 
< transMapEstV5 | <P>
< transMapEstV5 | This track follows the display conventions for 
< transMapEstV5 | <A HREF="../goldenPath/help/hgTracksHelp.html#PSLDisplay" 
< transMapEstV5 | TARGET=_blank>PSL alignment tracks</A>. </P>
< transMapEstV5 | <P>
< transMapEstV5 | This track may also be configured to display codon coloring, a feature that
< transMapEstV5 | allows the user to quickly compare cDNAs against the genomic sequence. For more 
< transMapEstV5 | information about this option, click 
< transMapEstV5 | <A HREF="../goldenPath/help/hgCodonColoringMrna.html" TARGET=_blank>here</A>.
< transMapEstV5 | Several types of alignment gap may also be colored; 
< transMapEstV5 | for more information, click 
< transMapEstV5 | <A HREF="../goldenPath/help/hgIndelDisplay.html" TARGET=_blank>here</A>.
< transMapEstV5 | 
< transMapEstV5 | <H2>Methods</H2>
< transMapEstV5 | 
< transMapEstV5 | <P>
< transMapEstV5 |   <ol>
< transMapEstV5 |     <li> Source transcript alignments were obtained from vertebrate organisms
< transMapEstV5 |     in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank 
< transMapEstV5 |     mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes,
< transMapEstV5 |     were used as available.
< transMapEstV5 |     <li> For all vertebrate assemblies that had BLASTZ alignment chains and
< transMapEstV5 |       nets to the bonobo (panPan2) genome, a subset of the alignment chains were
< transMapEstV5 |       selected as follows:
< transMapEstV5 |       <ul>
< transMapEstV5 |       <li> For organisms whose branch distance was no more than 0.5
< transMapEstV5 |         (as computed by <tt>phyloFit</tt>, see Conservation track description for details),
< transMapEstV5 |         syntenic filtering was used.  Reciprocal best nets were used if available;
< transMapEstV5 |         otherwise, nets were selected with the <tt>netfilter -syn</tt> command.
< transMapEstV5 |         The chains corresponding to the selected nets were used for mapping.
< transMapEstV5 |       <li> For more distant species, where the determination of synteny is difficult,
< transMapEstV5 |         the full set of chains was used for mapping. This allows for more genes to
< transMapEstV5 |         map at the expense of some mapping to paralogous regions.  The
< transMapEstV5 |         post-alignment filtering step removes some of the duplications.
< transMapEstV5 |     </ul>
< transMapEstV5 |     <li> The <tt>pslMap</tt> program was used to do a base-level projection of
< transMapEstV5 |       the source transcript alignments via the selected chains
< transMapEstV5 |       to the bonobo genome, resulting in pairwise alignments of the source transcripts to
< transMapEstV5 |       the genome.
< transMapEstV5 |     <li> The resulting alignments were filtered with <tt>pslCDnaFilter</tt>
< transMapEstV5 |       with a global near-best criteria of 0.5% in finished genomes
< transMapEstV5 |       (human and mouse) and 1.0% in other genomes.  Alignments
< transMapEstV5 |       where less than 20% of the transcript mapped were discarded.
< transMapEstV5 |   </ol>
< transMapEstV5 | </P>
< transMapEstV5 | 
< transMapEstV5 | <P>
< transMapEstV5 | To ensure unique identifiers for each alignment, cDNA and gene accessions were
< transMapEstV5 | made unique by appending a suffix for each location in the source genome and
< transMapEstV5 | again for each mapped location in the destination genome.  The format is:
< transMapEstV5 | <pre>
< transMapEstV5 |    accession.version-srcUniq.destUniq
< transMapEstV5 | </pre>
< transMapEstV5 | 
< transMapEstV5 | Where <tt>srcUniq</tt> is a number added to make each source alignment unique, and
< transMapEstV5 | <tt>destUniq</tt> is added to give the subsequent TransMap alignments unique
< transMapEstV5 | identifiers.
< transMapEstV5 | </P>
< transMapEstV5 | <P>
< transMapEstV5 | For example, in the cow genome, there are two alignments of mRNA <tt>BC149621.1</tt>.
< transMapEstV5 | These are assigned the identifiers <tt>BC149621.1-1</tt> and <tt>BC149621.1-2</tt>.
< transMapEstV5 | When these are mapped to the human genome, <tt>BC149621.1-1</tt> maps to a single
< transMapEstV5 | location and is given the identifier <tt>BC149621.1-1.1</tt>.  However, <tt>BC149621.1-2</tt>
< transMapEstV5 | maps to two locations, resulting in <tt>BC149621.1-2.1</tt> and <tt>BC149621.1-2.2</tt>.  Note
< transMapEstV5 | that multiple TransMap mappings are usually the result of tandem duplications, where both
< transMapEstV5 | chains are identified as syntenic.
< transMapEstV5 | </P>
< transMapEstV5 | 
< transMapEstV5 | <h2>Data Access</h2>
< transMapEstV5 | 
< transMapEstV5 | <p>
< transMapEstV5 | The raw data for these tracks can be accessed interactively through the
< transMapEstV5 | <a href="hgTables">Table Browser</a> or the
< transMapEstV5 | <a href="hgIntegrator">Data Integrator</a>.
< transMapEstV5 | For automated analysis, the annotations are stored in
< transMapEstV5 | <a href="../goldenPath/help/bigPsl.html">bigPsl</a> files (containing a
< transMapEstV5 | number of extra columns) and can be downloaded from our
< transMapEstV5 | <a href="http://hgdownload.soe.ucsc.edu/gbdb/panPan2/transMap/">download server</a>, 
< transMapEstV5 | or queried using our <a href="../goldenPath/help/api.html">API</a>. For more 
< transMapEstV5 | information on accessing track data see our 
< transMapEstV5 | <a href="../FAQ/FAQdownloads.html#download36">Track Data Access FAQ</a>.
< transMapEstV5 | The files are associated with these tracks in the following way:
< transMapEstV5 | <ul>
< transMapEstV5 | <li>TransMap Ensembl - <tt>panPan2.ensembl.transMapV4.bigPsl</tt></li>
< transMapEstV5 | <li>TransMap RefGene - <tt>panPan2.refseq.transMapV4.bigPsl</tt></li>
< transMapEstV5 | <li>TransMap RNA - <tt>panPan2.rna.transMapV4.bigPsl</tt></li>
< transMapEstV5 | <li>TransMap ESTs - <tt>panPan2.est.transMapV4.bigPsl</tt></li>
< transMapEstV5 | </ul>
< transMapEstV5 | Individual regions or the whole genome annotation can be obtained using our tool
< transMapEstV5 | <tt>bigBedToBed</tt> which can be compiled from the source code or downloaded as
< transMapEstV5 | a precompiled binary for your system. Instructions for downloading source code and
< transMapEstV5 | binaries can be found
< transMapEstV5 | <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>.
< transMapEstV5 | The tool can also be used to obtain only features within a given range, for example:
< transMapEstV5 | <p><tt>
< transMapEstV5 | bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/panPan2/transMap/V4/panPan2.refseq.transMapV4.bigPsl
< transMapEstV5 | -chrom=chr6 -start=0 -end=1000000 stdout
< transMapEstV5 | </tt>
< transMapEstV5 | 
< transMapEstV5 | <H2>Credits</H2>
< transMapEstV5 | 
< transMapEstV5 | <P>
< transMapEstV5 | This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data
< transMapEstV5 | submitted to the international public sequence databases by 
< transMapEstV5 | scientists worldwide and annotations produced by the RefSeq,
< transMapEstV5 | Ensembl, and GENCODE annotations projects.</P>
< transMapEstV5 | 
< transMapEstV5 | <H2>References</H2>
< transMapEstV5 | <p>
< transMapEstV5 | Siepel A, Diekhans M, Brejov&#225; B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S,
< transMapEstV5 | Lau C <em>et al</em>.
< transMapEstV5 | <a href="https://genome.cshlp.org/content/17/12/1763.long" target="_blank">
< transMapEstV5 | Targeted discovery of novel human exons by comparative genomics</a>.
< transMapEstV5 | <em>Genome Res</em>. 2007 Dec;17(12):1763-73.
< transMapEstV5 | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17989246" target="_blank">17989246</a>; PMC: <a
< transMapEstV5 | href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099585/" target="_blank">PMC2099585</a>
< transMapEstV5 | </p>
< transMapEstV5 | 
< transMapEstV5 | <p>
< transMapEstV5 | Stanke M, Diekhans M, Baertsch R, Haussler D.
< transMapEstV5 | <a href="https://academic.oup.com/bioinformatics/article/24/5/637/202844/Using-native-and-syntenically-mapped-cDNA"
< transMapEstV5 | target="_blank">
< transMapEstV5 | Using native and syntenically mapped cDNA alignments to improve de novo gene finding</a>.
< transMapEstV5 | <em>Bioinformatics</em>. 2008 Mar 1;24(5):637-44.
< transMapEstV5 | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18218656" target="_blank">18218656</a>
< transMapEstV5 | </p>
< transMapEstV5 | 
< transMapEstV5 | <p>
< transMapEstV5 | Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D.
< transMapEstV5 | <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030247"
< transMapEstV5 | target="_blank">
< transMapEstV5 | Comparative genomics search for losses of long-established genes on the human lineage</a>.
< transMapEstV5 | <em>PLoS Comput Biol</em>. 2007 Dec;3(12):e247.
< transMapEstV5 | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18085818" target="_blank">18085818</a>; PMC: <a
< transMapEstV5 | href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2134963/" target="_blank">PMC2134963</a>
< transMapEstV5 | </p>
< transMapEstV5 | 
< transMapEstV5 | 
< transMapRefSeqV5 | html
< transMapRefSeqV5 | <H2>Description</H2>
< transMapRefSeqV5 | 
< transMapRefSeqV5 | <P>
< transMapRefSeqV5 | This track contains RefSeq Gene alignments produced by
< transMapRefSeqV5 | the <em>TransMap</em> cross-species alignment algorithm
< transMapRefSeqV5 | from other vertebrate species in the UCSC Genome Browser.
< transMapRefSeqV5 | For closer evolutionary distances, the alignments are created using
< transMapRefSeqV5 | syntenically filtered BLASTZ alignment chains, resulting in a prediction of the
< transMapRefSeqV5 | orthologous genes in bonobo.
< transMapRefSeqV5 | </P>
< transMapRefSeqV5 | 
< transMapRefSeqV5 | 
< transMapRefSeqV5 | <H2>Display Conventions and Configuration</H2>
< transMapRefSeqV5 | 
< transMapRefSeqV5 | <P>
< transMapRefSeqV5 | This track follows the display conventions for 
< transMapRefSeqV5 | <A HREF="../goldenPath/help/hgTracksHelp.html#PSLDisplay" 
< transMapRefSeqV5 | TARGET=_blank>PSL alignment tracks</A>. </P>
< transMapRefSeqV5 | <P>
< transMapRefSeqV5 | This track may also be configured to display codon coloring, a feature that
< transMapRefSeqV5 | allows the user to quickly compare cDNAs against the genomic sequence. For more 
< transMapRefSeqV5 | information about this option, click 
< transMapRefSeqV5 | <A HREF="../goldenPath/help/hgCodonColoringMrna.html" TARGET=_blank>here</A>.
< transMapRefSeqV5 | Several types of alignment gap may also be colored; 
< transMapRefSeqV5 | for more information, click 
< transMapRefSeqV5 | <A HREF="../goldenPath/help/hgIndelDisplay.html" TARGET=_blank>here</A>.
< transMapRefSeqV5 | 
< transMapRefSeqV5 | <H2>Methods</H2>
< transMapRefSeqV5 | 
< transMapRefSeqV5 | <P>
< transMapRefSeqV5 |   <ol>
< transMapRefSeqV5 |     <li> Source transcript alignments were obtained from vertebrate organisms
< transMapRefSeqV5 |     in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank 
< transMapRefSeqV5 |     mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes,
< transMapRefSeqV5 |     were used as available.
< transMapRefSeqV5 |     <li> For all vertebrate assemblies that had BLASTZ alignment chains and
< transMapRefSeqV5 |       nets to the bonobo (panPan2) genome, a subset of the alignment chains were
< transMapRefSeqV5 |       selected as follows:
< transMapRefSeqV5 |       <ul>
< transMapRefSeqV5 |       <li> For organisms whose branch distance was no more than 0.5
< transMapRefSeqV5 |         (as computed by <tt>phyloFit</tt>, see Conservation track description for details),
< transMapRefSeqV5 |         syntenic filtering was used.  Reciprocal best nets were used if available;
< transMapRefSeqV5 |         otherwise, nets were selected with the <tt>netfilter -syn</tt> command.
< transMapRefSeqV5 |         The chains corresponding to the selected nets were used for mapping.
< transMapRefSeqV5 |       <li> For more distant species, where the determination of synteny is difficult,
< transMapRefSeqV5 |         the full set of chains was used for mapping. This allows for more genes to
< transMapRefSeqV5 |         map at the expense of some mapping to paralogous regions.  The
< transMapRefSeqV5 |         post-alignment filtering step removes some of the duplications.
< transMapRefSeqV5 |     </ul>
< transMapRefSeqV5 |     <li> The <tt>pslMap</tt> program was used to do a base-level projection of
< transMapRefSeqV5 |       the source transcript alignments via the selected chains
< transMapRefSeqV5 |       to the bonobo genome, resulting in pairwise alignments of the source transcripts to
< transMapRefSeqV5 |       the genome.
< transMapRefSeqV5 |     <li> The resulting alignments were filtered with <tt>pslCDnaFilter</tt>
< transMapRefSeqV5 |       with a global near-best criteria of 0.5% in finished genomes
< transMapRefSeqV5 |       (human and mouse) and 1.0% in other genomes.  Alignments
< transMapRefSeqV5 |       where less than 20% of the transcript mapped were discarded.
< transMapRefSeqV5 |   </ol>
< transMapRefSeqV5 | </P>
< transMapRefSeqV5 | 
< transMapRefSeqV5 | <P>
< transMapRefSeqV5 | To ensure unique identifiers for each alignment, cDNA and gene accessions were
< transMapRefSeqV5 | made unique by appending a suffix for each location in the source genome and
< transMapRefSeqV5 | again for each mapped location in the destination genome.  The format is:
< transMapRefSeqV5 | <pre>
< transMapRefSeqV5 |    accession.version-srcUniq.destUniq
< transMapRefSeqV5 | </pre>
< transMapRefSeqV5 | 
< transMapRefSeqV5 | Where <tt>srcUniq</tt> is a number added to make each source alignment unique, and
< transMapRefSeqV5 | <tt>destUniq</tt> is added to give the subsequent TransMap alignments unique
< transMapRefSeqV5 | identifiers.
< transMapRefSeqV5 | </P>
< transMapRefSeqV5 | <P>
< transMapRefSeqV5 | For example, in the cow genome, there are two alignments of mRNA <tt>BC149621.1</tt>.
< transMapRefSeqV5 | These are assigned the identifiers <tt>BC149621.1-1</tt> and <tt>BC149621.1-2</tt>.
< transMapRefSeqV5 | When these are mapped to the human genome, <tt>BC149621.1-1</tt> maps to a single
< transMapRefSeqV5 | location and is given the identifier <tt>BC149621.1-1.1</tt>.  However, <tt>BC149621.1-2</tt>
< transMapRefSeqV5 | maps to two locations, resulting in <tt>BC149621.1-2.1</tt> and <tt>BC149621.1-2.2</tt>.  Note
< transMapRefSeqV5 | that multiple TransMap mappings are usually the result of tandem duplications, where both
< transMapRefSeqV5 | chains are identified as syntenic.
< transMapRefSeqV5 | </P>
< transMapRefSeqV5 | 
< transMapRefSeqV5 | <h2>Data Access</h2>
< transMapRefSeqV5 | 
< transMapRefSeqV5 | <p>
< transMapRefSeqV5 | The raw data for these tracks can be accessed interactively through the
< transMapRefSeqV5 | <a href="hgTables">Table Browser</a> or the
< transMapRefSeqV5 | <a href="hgIntegrator">Data Integrator</a>.
< transMapRefSeqV5 | For automated analysis, the annotations are stored in
< transMapRefSeqV5 | <a href="../goldenPath/help/bigPsl.html">bigPsl</a> files (containing a
< transMapRefSeqV5 | number of extra columns) and can be downloaded from our
< transMapRefSeqV5 | <a href="http://hgdownload.soe.ucsc.edu/gbdb/panPan2/transMap/">download server</a>, 
< transMapRefSeqV5 | or queried using our <a href="../goldenPath/help/api.html">API</a>. For more 
< transMapRefSeqV5 | information on accessing track data see our 
< transMapRefSeqV5 | <a href="../FAQ/FAQdownloads.html#download36">Track Data Access FAQ</a>.
< transMapRefSeqV5 | The files are associated with these tracks in the following way:
< transMapRefSeqV5 | <ul>
< transMapRefSeqV5 | <li>TransMap Ensembl - <tt>panPan2.ensembl.transMapV4.bigPsl</tt></li>
< transMapRefSeqV5 | <li>TransMap RefGene - <tt>panPan2.refseq.transMapV4.bigPsl</tt></li>
< transMapRefSeqV5 | <li>TransMap RNA - <tt>panPan2.rna.transMapV4.bigPsl</tt></li>
< transMapRefSeqV5 | <li>TransMap ESTs - <tt>panPan2.est.transMapV4.bigPsl</tt></li>
< transMapRefSeqV5 | </ul>
< transMapRefSeqV5 | Individual regions or the whole genome annotation can be obtained using our tool
< transMapRefSeqV5 | <tt>bigBedToBed</tt> which can be compiled from the source code or downloaded as
< transMapRefSeqV5 | a precompiled binary for your system. Instructions for downloading source code and
< transMapRefSeqV5 | binaries can be found
< transMapRefSeqV5 | <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>.
< transMapRefSeqV5 | The tool can also be used to obtain only features within a given range, for example:
< transMapRefSeqV5 | <p><tt>
< transMapRefSeqV5 | bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/panPan2/transMap/V4/panPan2.refseq.transMapV4.bigPsl
< transMapRefSeqV5 | -chrom=chr6 -start=0 -end=1000000 stdout
< transMapRefSeqV5 | </tt>
< transMapRefSeqV5 | 
< transMapRefSeqV5 | <H2>Credits</H2>
< transMapRefSeqV5 | 
< transMapRefSeqV5 | <P>
< transMapRefSeqV5 | This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data
< transMapRefSeqV5 | submitted to the international public sequence databases by 
< transMapRefSeqV5 | scientists worldwide and annotations produced by the RefSeq,
< transMapRefSeqV5 | Ensembl, and GENCODE annotations projects.</P>
< transMapRefSeqV5 | 
< transMapRefSeqV5 | <H2>References</H2>
< transMapRefSeqV5 | <p>
< transMapRefSeqV5 | Siepel A, Diekhans M, Brejov&#225; B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S,
< transMapRefSeqV5 | Lau C <em>et al</em>.
< transMapRefSeqV5 | <a href="https://genome.cshlp.org/content/17/12/1763.long" target="_blank">
< transMapRefSeqV5 | Targeted discovery of novel human exons by comparative genomics</a>.
< transMapRefSeqV5 | <em>Genome Res</em>. 2007 Dec;17(12):1763-73.
< transMapRefSeqV5 | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17989246" target="_blank">17989246</a>; PMC: <a
< transMapRefSeqV5 | href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099585/" target="_blank">PMC2099585</a>
< transMapRefSeqV5 | </p>
< transMapRefSeqV5 | 
< transMapRefSeqV5 | <p>
< transMapRefSeqV5 | Stanke M, Diekhans M, Baertsch R, Haussler D.
< transMapRefSeqV5 | <a href="https://academic.oup.com/bioinformatics/article/24/5/637/202844/Using-native-and-syntenically-mapped-cDNA"
< transMapRefSeqV5 | target="_blank">
< transMapRefSeqV5 | Using native and syntenically mapped cDNA alignments to improve de novo gene finding</a>.
< transMapRefSeqV5 | <em>Bioinformatics</em>. 2008 Mar 1;24(5):637-44.
< transMapRefSeqV5 | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18218656" target="_blank">18218656</a>
< transMapRefSeqV5 | </p>
< transMapRefSeqV5 | 
< transMapRefSeqV5 | <p>
< transMapRefSeqV5 | Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D.
< transMapRefSeqV5 | <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030247"
< transMapRefSeqV5 | target="_blank">
< transMapRefSeqV5 | Comparative genomics search for losses of long-established genes on the human lineage</a>.
< transMapRefSeqV5 | <em>PLoS Comput Biol</em>. 2007 Dec;3(12):e247.
< transMapRefSeqV5 | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18085818" target="_blank">18085818</a>; PMC: <a
< transMapRefSeqV5 | href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2134963/" target="_blank">PMC2134963</a>
< transMapRefSeqV5 | </p>
< transMapRefSeqV5 | 
< transMapRefSeqV5 | 
< transMapRnaV5 | html
< transMapRnaV5 | <H2>Description</H2>
< transMapRnaV5 | 
< transMapRnaV5 | <P>
< transMapRnaV5 | This track contains GenBank mRNA alignments produced by
< transMapRnaV5 | the <em>TransMap</em> cross-species alignment algorithm
< transMapRnaV5 | from other vertebrate species in the UCSC Genome Browser.
< transMapRnaV5 | For closer evolutionary distances, the alignments are created using
< transMapRnaV5 | syntenically filtered BLASTZ alignment chains, resulting in a prediction of the
< transMapRnaV5 | orthologous genes in bonobo.
< transMapRnaV5 | </P>
< transMapRnaV5 | 
< transMapRnaV5 | 
< transMapRnaV5 | <H2>Display Conventions and Configuration</H2>
< transMapRnaV5 | 
< transMapRnaV5 | <P>
< transMapRnaV5 | This track follows the display conventions for 
< transMapRnaV5 | <A HREF="../goldenPath/help/hgTracksHelp.html#PSLDisplay" 
< transMapRnaV5 | TARGET=_blank>PSL alignment tracks</A>. </P>
< transMapRnaV5 | <P>
< transMapRnaV5 | This track may also be configured to display codon coloring, a feature that
< transMapRnaV5 | allows the user to quickly compare cDNAs against the genomic sequence. For more 
< transMapRnaV5 | information about this option, click 
< transMapRnaV5 | <A HREF="../goldenPath/help/hgCodonColoringMrna.html" TARGET=_blank>here</A>.
< transMapRnaV5 | Several types of alignment gap may also be colored; 
< transMapRnaV5 | for more information, click 
< transMapRnaV5 | <A HREF="../goldenPath/help/hgIndelDisplay.html" TARGET=_blank>here</A>.
< transMapRnaV5 | 
< transMapRnaV5 | <H2>Methods</H2>
< transMapRnaV5 | 
< transMapRnaV5 | <P>
< transMapRnaV5 |   <ol>
< transMapRnaV5 |     <li> Source transcript alignments were obtained from vertebrate organisms
< transMapRnaV5 |     in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank 
< transMapRnaV5 |     mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes,
< transMapRnaV5 |     were used as available.
< transMapRnaV5 |     <li> For all vertebrate assemblies that had BLASTZ alignment chains and
< transMapRnaV5 |       nets to the bonobo (panPan2) genome, a subset of the alignment chains were
< transMapRnaV5 |       selected as follows:
< transMapRnaV5 |       <ul>
< transMapRnaV5 |       <li> For organisms whose branch distance was no more than 0.5
< transMapRnaV5 |         (as computed by <tt>phyloFit</tt>, see Conservation track description for details),
< transMapRnaV5 |         syntenic filtering was used.  Reciprocal best nets were used if available;
< transMapRnaV5 |         otherwise, nets were selected with the <tt>netfilter -syn</tt> command.
< transMapRnaV5 |         The chains corresponding to the selected nets were used for mapping.
< transMapRnaV5 |       <li> For more distant species, where the determination of synteny is difficult,
< transMapRnaV5 |         the full set of chains was used for mapping. This allows for more genes to
< transMapRnaV5 |         map at the expense of some mapping to paralogous regions.  The
< transMapRnaV5 |         post-alignment filtering step removes some of the duplications.
< transMapRnaV5 |     </ul>
< transMapRnaV5 |     <li> The <tt>pslMap</tt> program was used to do a base-level projection of
< transMapRnaV5 |       the source transcript alignments via the selected chains
< transMapRnaV5 |       to the bonobo genome, resulting in pairwise alignments of the source transcripts to
< transMapRnaV5 |       the genome.
< transMapRnaV5 |     <li> The resulting alignments were filtered with <tt>pslCDnaFilter</tt>
< transMapRnaV5 |       with a global near-best criteria of 0.5% in finished genomes
< transMapRnaV5 |       (human and mouse) and 1.0% in other genomes.  Alignments
< transMapRnaV5 |       where less than 20% of the transcript mapped were discarded.
< transMapRnaV5 |   </ol>
< transMapRnaV5 | </P>
< transMapRnaV5 | 
< transMapRnaV5 | <P>
< transMapRnaV5 | To ensure unique identifiers for each alignment, cDNA and gene accessions were
< transMapRnaV5 | made unique by appending a suffix for each location in the source genome and
< transMapRnaV5 | again for each mapped location in the destination genome.  The format is:
< transMapRnaV5 | <pre>
< transMapRnaV5 |    accession.version-srcUniq.destUniq
< transMapRnaV5 | </pre>
< transMapRnaV5 | 
< transMapRnaV5 | Where <tt>srcUniq</tt> is a number added to make each source alignment unique, and
< transMapRnaV5 | <tt>destUniq</tt> is added to give the subsequent TransMap alignments unique
< transMapRnaV5 | identifiers.
< transMapRnaV5 | </P>
< transMapRnaV5 | <P>
< transMapRnaV5 | For example, in the cow genome, there are two alignments of mRNA <tt>BC149621.1</tt>.
< transMapRnaV5 | These are assigned the identifiers <tt>BC149621.1-1</tt> and <tt>BC149621.1-2</tt>.
< transMapRnaV5 | When these are mapped to the human genome, <tt>BC149621.1-1</tt> maps to a single
< transMapRnaV5 | location and is given the identifier <tt>BC149621.1-1.1</tt>.  However, <tt>BC149621.1-2</tt>
< transMapRnaV5 | maps to two locations, resulting in <tt>BC149621.1-2.1</tt> and <tt>BC149621.1-2.2</tt>.  Note
< transMapRnaV5 | that multiple TransMap mappings are usually the result of tandem duplications, where both
< transMapRnaV5 | chains are identified as syntenic.
< transMapRnaV5 | </P>
< transMapRnaV5 | 
< transMapRnaV5 | <h2>Data Access</h2>
< transMapRnaV5 | 
< transMapRnaV5 | <p>
< transMapRnaV5 | The raw data for these tracks can be accessed interactively through the
< transMapRnaV5 | <a href="hgTables">Table Browser</a> or the
< transMapRnaV5 | <a href="hgIntegrator">Data Integrator</a>.
< transMapRnaV5 | For automated analysis, the annotations are stored in
< transMapRnaV5 | <a href="../goldenPath/help/bigPsl.html">bigPsl</a> files (containing a
< transMapRnaV5 | number of extra columns) and can be downloaded from our
< transMapRnaV5 | <a href="http://hgdownload.soe.ucsc.edu/gbdb/panPan2/transMap/">download server</a>, 
< transMapRnaV5 | or queried using our <a href="../goldenPath/help/api.html">API</a>. For more 
< transMapRnaV5 | information on accessing track data see our 
< transMapRnaV5 | <a href="../FAQ/FAQdownloads.html#download36">Track Data Access FAQ</a>.
< transMapRnaV5 | The files are associated with these tracks in the following way:
< transMapRnaV5 | <ul>
< transMapRnaV5 | <li>TransMap Ensembl - <tt>panPan2.ensembl.transMapV4.bigPsl</tt></li>
< transMapRnaV5 | <li>TransMap RefGene - <tt>panPan2.refseq.transMapV4.bigPsl</tt></li>
< transMapRnaV5 | <li>TransMap RNA - <tt>panPan2.rna.transMapV4.bigPsl</tt></li>
< transMapRnaV5 | <li>TransMap ESTs - <tt>panPan2.est.transMapV4.bigPsl</tt></li>
< transMapRnaV5 | </ul>
< transMapRnaV5 | Individual regions or the whole genome annotation can be obtained using our tool
< transMapRnaV5 | <tt>bigBedToBed</tt> which can be compiled from the source code or downloaded as
< transMapRnaV5 | a precompiled binary for your system. Instructions for downloading source code and
< transMapRnaV5 | binaries can be found
< transMapRnaV5 | <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>.
< transMapRnaV5 | The tool can also be used to obtain only features within a given range, for example:
< transMapRnaV5 | <p><tt>
< transMapRnaV5 | bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/panPan2/transMap/V4/panPan2.refseq.transMapV4.bigPsl
< transMapRnaV5 | -chrom=chr6 -start=0 -end=1000000 stdout
< transMapRnaV5 | </tt>
< transMapRnaV5 | 
< transMapRnaV5 | <H2>Credits</H2>
< transMapRnaV5 | 
< transMapRnaV5 | <P>
< transMapRnaV5 | This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data
< transMapRnaV5 | submitted to the international public sequence databases by 
< transMapRnaV5 | scientists worldwide and annotations produced by the RefSeq,
< transMapRnaV5 | Ensembl, and GENCODE annotations projects.</P>
< transMapRnaV5 | 
< transMapRnaV5 | <H2>References</H2>
< transMapRnaV5 | <p>
< transMapRnaV5 | Siepel A, Diekhans M, Brejov&#225; B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S,
< transMapRnaV5 | Lau C <em>et al</em>.
< transMapRnaV5 | <a href="https://genome.cshlp.org/content/17/12/1763.long" target="_blank">
< transMapRnaV5 | Targeted discovery of novel human exons by comparative genomics</a>.
< transMapRnaV5 | <em>Genome Res</em>. 2007 Dec;17(12):1763-73.
< transMapRnaV5 | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17989246" target="_blank">17989246</a>; PMC: <a
< transMapRnaV5 | href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099585/" target="_blank">PMC2099585</a>
< transMapRnaV5 | </p>
< transMapRnaV5 | 
< transMapRnaV5 | <p>
< transMapRnaV5 | Stanke M, Diekhans M, Baertsch R, Haussler D.
< transMapRnaV5 | <a href="https://academic.oup.com/bioinformatics/article/24/5/637/202844/Using-native-and-syntenically-mapped-cDNA"
< transMapRnaV5 | target="_blank">
< transMapRnaV5 | Using native and syntenically mapped cDNA alignments to improve de novo gene finding</a>.
< transMapRnaV5 | <em>Bioinformatics</em>. 2008 Mar 1;24(5):637-44.
< transMapRnaV5 | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18218656" target="_blank">18218656</a>
< transMapRnaV5 | </p>
< transMapRnaV5 | 
< transMapRnaV5 | <p>
< transMapRnaV5 | Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D.
< transMapRnaV5 | <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030247"
< transMapRnaV5 | target="_blank">
< transMapRnaV5 | Comparative genomics search for losses of long-established genes on the human lineage</a>.
< transMapRnaV5 | <em>PLoS Comput Biol</em>. 2007 Dec;3(12):e247.
< transMapRnaV5 | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18085818" target="_blank">18085818</a>; PMC: <a
< transMapRnaV5 | href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2134963/" target="_blank">PMC2134963</a>
< transMapRnaV5 | </p>
< transMapRnaV5 | 
< transMapRnaV5 | 
< transMapV5 | html
< transMapV5 | <H2>Description</H2>
< transMapV5 | 
< transMapV5 | <P>
< transMapV5 | These tracks contain cDNA and gene alignments produced by
< transMapV5 | the <em>TransMap</em> cross-species alignment algorithm
< transMapV5 | from other vertebrate species in the UCSC Genome Browser.
< transMapV5 | For closer evolutionary distances, the alignments are created using
< transMapV5 | syntenically filtered LASTZ or BLASTZ alignment chains, resulting
< transMapV5 | in a prediction of the orthologous genes in bonobo.  For more distant
< transMapV5 | organisms, reciprocal best alignments are used.
< transMapV5 | </P>
< transMapV5 | 
< transMapV5 | <em>TransMap</em> maps genes and related annotations in one species to another
< transMapV5 | using synteny-filtered pairwise genome alignments (chains and nets) to
< transMapV5 | determine the most likely orthologs.  For example, for the mRNA TransMap track
< transMapV5 | on the human assembly, more than 400,000 mRNAs from 25 vertebrate species were
< transMapV5 | aligned at high stringency to the native assembly using BLAT.  The alignments
< transMapV5 | were then mapped to the human assembly using the chain and net alignments
< transMapV5 | produced using BLASTZ, which has higher sensitivity than BLAT for diverged
< transMapV5 | organisms.
< transMapV5 | <P>
< transMapV5 | Compared to translated BLAT, TransMap finds fewer paralogs and aligns more UTR
< transMapV5 | bases.
< transMapV5 | </P>
< transMapV5 | 
< transMapV5 | <H2>Display Conventions and Configuration</H2>
< transMapV5 | 
< transMapV5 | <P>
< transMapV5 | This track follows the display conventions for 
< transMapV5 | <A HREF="../goldenPath/help/hgTracksHelp.html#PSLDisplay" 
< transMapV5 | TARGET=_blank>PSL alignment tracks</A>. </P>
< transMapV5 | <P>
< transMapV5 | This track may also be configured to display codon coloring, a feature that
< transMapV5 | allows the user to quickly compare cDNAs against the genomic sequence. For more 
< transMapV5 | information about this option, click 
< transMapV5 | <A HREF="../goldenPath/help/hgCodonColoringMrna.html" TARGET=_blank>here</A>.
< transMapV5 | Several types of alignment gap may also be colored; 
< transMapV5 | for more information, click 
< transMapV5 | <A HREF="../goldenPath/help/hgIndelDisplay.html" TARGET=_blank>here</A>.
< transMapV5 | 
< transMapV5 | <H2>Methods</H2>
< transMapV5 | 
< transMapV5 | <P>
< transMapV5 |   <ol>
< transMapV5 |     <li> Source transcript alignments were obtained from vertebrate organisms
< transMapV5 |     in the UCSC Genome Browser Database. BLAT alignments of RefSeq Genes, GenBank 
< transMapV5 |     mRNAs, and GenBank Spliced ESTs to the cognate genome, along with UCSC Genes,
< transMapV5 |     were used as available.
< transMapV5 |     <li> For all vertebrate assemblies that had BLASTZ alignment chains and
< transMapV5 |       nets to the bonobo (panPan2) genome, a subset of the alignment chains were
< transMapV5 |       selected as follows:
< transMapV5 |       <ul>
< transMapV5 |       <li> For organisms whose branch distance was no more than 0.5
< transMapV5 |         (as computed by <tt>phyloFit</tt>, see Conservation track description for details),
< transMapV5 |         syntenic filtering was used.  Reciprocal best nets were used if available;
< transMapV5 |         otherwise, nets were selected with the <tt>netfilter -syn</tt> command.
< transMapV5 |         The chains corresponding to the selected nets were used for mapping.
< transMapV5 |       <li> For more distant species, where the determination of synteny is difficult,
< transMapV5 |         the full set of chains was used for mapping. This allows for more genes to
< transMapV5 |         map at the expense of some mapping to paralogous regions.  The
< transMapV5 |         post-alignment filtering step removes some of the duplications.
< transMapV5 |     </ul>
< transMapV5 |     <li> The <tt>pslMap</tt> program was used to do a base-level projection of
< transMapV5 |       the source transcript alignments via the selected chains
< transMapV5 |       to the bonobo genome, resulting in pairwise alignments of the source transcripts to
< transMapV5 |       the genome.
< transMapV5 |     <li> The resulting alignments were filtered with <tt>pslCDnaFilter</tt>
< transMapV5 |       with a global near-best criteria of 0.5% in finished genomes
< transMapV5 |       (human and mouse) and 1.0% in other genomes.  Alignments
< transMapV5 |       where less than 20% of the transcript mapped were discarded.
< transMapV5 |   </ol>
< transMapV5 | </P>
< transMapV5 | 
< transMapV5 | <P>
< transMapV5 | To ensure unique identifiers for each alignment, cDNA and gene accessions were
< transMapV5 | made unique by appending a suffix for each location in the source genome and
< transMapV5 | again for each mapped location in the destination genome.  The format is:
< transMapV5 | <pre>
< transMapV5 |    accession.version-srcUniq.destUniq
< transMapV5 | </pre>
< transMapV5 | 
< transMapV5 | Where <tt>srcUniq</tt> is a number added to make each source alignment unique, and
< transMapV5 | <tt>destUniq</tt> is added to give the subsequent TransMap alignments unique
< transMapV5 | identifiers.
< transMapV5 | </P>
< transMapV5 | <P>
< transMapV5 | For example, in the cow genome, there are two alignments of mRNA <tt>BC149621.1</tt>.
< transMapV5 | These are assigned the identifiers <tt>BC149621.1-1</tt> and <tt>BC149621.1-2</tt>.
< transMapV5 | When these are mapped to the human genome, <tt>BC149621.1-1</tt> maps to a single
< transMapV5 | location and is given the identifier <tt>BC149621.1-1.1</tt>.  However, <tt>BC149621.1-2</tt>
< transMapV5 | maps to two locations, resulting in <tt>BC149621.1-2.1</tt> and <tt>BC149621.1-2.2</tt>.  Note
< transMapV5 | that multiple TransMap mappings are usually the result of tandem duplications, where both
< transMapV5 | chains are identified as syntenic.
< transMapV5 | </P>
< transMapV5 | 
< transMapV5 | <h2>Data Access</h2>
< transMapV5 | 
< transMapV5 | <p>
< transMapV5 | The raw data for these tracks can be accessed interactively through the
< transMapV5 | <a href="hgTables">Table Browser</a> or the
< transMapV5 | <a href="hgIntegrator">Data Integrator</a>.
< transMapV5 | For automated analysis, the annotations are stored in
< transMapV5 | <a href="../goldenPath/help/bigPsl.html">bigPsl</a> files (containing a
< transMapV5 | number of extra columns) and can be downloaded from our
< transMapV5 | <a href="http://hgdownload.soe.ucsc.edu/gbdb/panPan2/transMap/">download server</a>, 
< transMapV5 | or queried using our <a href="../goldenPath/help/api.html">API</a>. For more 
< transMapV5 | information on accessing track data see our 
< transMapV5 | <a href="../FAQ/FAQdownloads.html#download36">Track Data Access FAQ</a>.
< transMapV5 | The files are associated with these tracks in the following way:
< transMapV5 | <ul>
< transMapV5 | <li>TransMap Ensembl - <tt>panPan2.ensembl.transMapV5.bigPsl</tt></li>
< transMapV5 | <li>TransMap RefGene - <tt>panPan2.refseq.transMapV5.bigPsl</tt></li>
< transMapV5 | <li>TransMap RNA - <tt>panPan2.rna.transMapV5.bigPsl</tt></li>
< transMapV5 | <li>TransMap ESTs - <tt>panPan2.est.transMapV5.bigPsl</tt></li>
< transMapV5 | </ul>
< transMapV5 | Individual regions or the whole genome annotation can be obtained using our tool
< transMapV5 | <tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded as
< transMapV5 | a precompiled binary for your system. Instructions for downloading source code and
< transMapV5 | binaries can be found
< transMapV5 | <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>.
< transMapV5 | The tool can also be used to obtain only features within a given range, for example:
< transMapV5 | <p><tt>
< transMapV5 | bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/panPan2/transMap/V5/panPan2.refseq.transMapV5.bigPsl
< transMapV5 | -chrom=chr6 -start=0 -end=1000000 stdout
< transMapV5 | </tt>
< transMapV5 | 
< transMapV5 | <H2>Credits</H2>
< transMapV5 | 
< transMapV5 | <P>
< transMapV5 | This track was produced by Mark Diekhans at UCSC from cDNA and EST sequence data
< transMapV5 | submitted to the international public sequence databases by 
< transMapV5 | scientists worldwide and annotations produced by the RefSeq,
< transMapV5 | Ensembl, and GENCODE annotations projects.</P>
< transMapV5 | 
< transMapV5 | <H2>References</H2>
< transMapV5 | <p>
< transMapV5 | Siepel A, Diekhans M, Brejov&#225; B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S,
< transMapV5 | Lau C <em>et al</em>.
< transMapV5 | <a href="https://genome.cshlp.org/content/17/12/1763.long" target="_blank">
< transMapV5 | Targeted discovery of novel human exons by comparative genomics</a>.
< transMapV5 | <em>Genome Res</em>. 2007 Dec;17(12):1763-73.
< transMapV5 | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17989246" target="_blank">17989246</a>; PMC: <a
< transMapV5 | href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099585/" target="_blank">PMC2099585</a>
< transMapV5 | </p>
< transMapV5 | 
< transMapV5 | <p>
< transMapV5 | Stanke M, Diekhans M, Baertsch R, Haussler D.
< transMapV5 | <a href="https://academic.oup.com/bioinformatics/article/24/5/637/202844/Using-native-and-syntenically-mapped-cDNA"
< transMapV5 | target="_blank">
< transMapV5 | Using native and syntenically mapped cDNA alignments to improve de novo gene finding</a>.
< transMapV5 | <em>Bioinformatics</em>. 2008 Mar 1;24(5):637-44.
< transMapV5 | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18218656" target="_blank">18218656</a>
< transMapV5 | </p>
< transMapV5 | 
< transMapV5 | <p>
< transMapV5 | Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D.
< transMapV5 | <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030247"
< transMapV5 | target="_blank">
< transMapV5 | Comparative genomics search for losses of long-established genes on the human lineage</a>.
< transMapV5 | <em>PLoS Comput Biol</em>. 2007 Dec;3(12):e247.
< transMapV5 | PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18085818" target="_blank">18085818</a>; PMC: <a
< transMapV5 | href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2134963/" target="_blank">PMC2134963</a>
< transMapV5 | </p>
< transMapV5 | 
< transMapV5 |