Index: src/hg/makeDb/trackDb/transMap.html
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RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/transMap.html,v
retrieving revision 1.14
retrieving revision 1.15
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--- src/hg/makeDb/trackDb/transMap.html	20 Sep 2009 17:24:35 -0000	1.14
+++ src/hg/makeDb/trackDb/transMap.html	17 Dec 2009 18:43:38 -0000	1.15
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 <H2>Description</H2>
 <P>
 These tracks contain cDNA and gene alignments produced by
 the <em>TransMap</em> cross-species alignment algorithm
 from other vertebrate species in the UCSC Genome Browser.
 For closer evolutionary distances, the alignments are created using
 syntenically filtered BLASTZ alignment chains, resulting in a prediction of the
 orthologous genes in $organism.
 </P>
 
 <em>TransMap</em> maps genes and related annotations in one species to another
 using synteny-filtered pairwise genome alignments (chains and nets) to
 determine the most likely orthologs.  For example, for the mRNA TransMap track
 on the human assembly, more than 400,000 mRNAs from 25 vertebrate species were
 aligned at high stringency to the native assembly using BLAT.  The alignments
 were then mapped to the human assembly using the chain and net alignments
 produced using blastz, which has higher sensitivity than BLAT for diverged
 organisms.
 <P>
 Compared to translated BLAT, TransMap finds fewer paralogs and aligns more UTR
 bases.  For closely related low-coverage assemblies, a reciprocal-best
 relationship is used in the chains and nets to improve the synteny prediction.
 </P>
 
 <!-- everything below here common to all transMap*.html pages -->
 <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 (bosTau4) genome, there are two alignments of mRNA <tt>BC149621.1</tt>.
+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 (hg18) genome, <tt>BC149621.1-1</tt> maps to a single
+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>Credits</H2>
 <P>
 This track was produced by Mark Diekhans at UCSC from cDNA sequence data
 submitted to the international public sequence databases by 
 scientists worldwide.</P>
 
 <H2>References</H2>
 <P>
 Zhu J, Sanborn JZ, Diekhans M, Lowe CB, Pringle TH, Haussler D. 
 <A HREF="http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0030247.eor"
 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.</P>
 <P>
 Stanke M, Diekhans M, Baertsch R, Haussler D.
 <A HREF="http://bioinformatics.oxfordjournals.org/cgi/content/full/24/5/637"
 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.</P>
 <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="http://www.genome.org/cgi/content/abstract/gr.7128207v1"
 TARGET=_blank>Targeted discovery of novel human exons by comparative 
 genomics</A>.
 <em>Genome Res.</em> 2007 Dec;17(12):1763-73.</P>
 

