src/hg/makeDb/trackDb/sibGene.html 1.3

Index: src/hg/makeDb/trackDb/sibGene.html
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RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/sibGene.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/makeDb/trackDb/sibGene.html	31 Aug 2007 18:57:31 -0000	1.2
+++ src/hg/makeDb/trackDb/sibGene.html	23 Jan 2010 00:53:45 -0000	1.3
@@ -1,71 +1,71 @@
 <H2>Description</H2>
 <P>
 The SIB Genes track shows gene predictions based on data
 from RefSeq and EMBL/GenBank.  This is transcript-based set of
 predictions. Genes all have the support of at least one GenBank full length RNA sequence,
 one RefSeq RNA, or one spliced EST.  The track includes both protein-coding
 and non-coding transcripts.  The coding regions are predicted using
 <A HREF="http://estscan.sourceforge.net" TARGET = _BLANK>ESTScan</A>.</P>
 
 <H2>Display Conventions and Configuration</H2>
 <P>
 This track in general follows the display conventions for
 <A HREF="../goldenPath/help/hgTracksHelp.html#GeneDisplay">gene prediction
 tracks</A>.  The exons for putative noncoding genes and untranslated regions 
 are represented by relatively thin blocks, while those for coding open 
 reading frames are thicker.</P>
 <P>
 This track contains an optional codon coloring
 feature that allows users to quickly validate and compare gene predictions.
 To display codon colors, select the <em>genomic codons</em> option from the
 <em>Color track by codons</em> pull-down menu.  Click
 <A HREF="../goldenPath/help/hgCodonColoring.html">here</A> for more
 information about this feature. </P>
 <P>Further information on the predicted transcripts can be found on the
 <A HREF="http://www.isrec.isb-sib.ch/tromer/" TARGET = _BLANK>Transcriptome Web
 interface</A>.</P>
 
 
 <H2>Methods</H2>
 <P>
 The SIB Genes are built using a multi-step pipeline:  
 <OL>
 <LI>RefSeq and GenBank RNAs and ESTs are aligned to the genome with
 <A HREF="http://sibsim4.sourceforge.net" TARGET = _BLANK>SIBsim4</A>, keeping 
 only the best alignments for each RNA.
 <LI>Alignments are broken up at non-intronic gaps, with small isolated 
 fragments thrown out.
 <LI>A splicing graph is created for each set of overlapping alignments. This
 graph has an edge for each exon or intron, and a vertex for each splice site,
 start, and end.  Each RNA that contributes to an edge is kept as evidence for
 that edge.
 <LI>The graph is traversed to generate all unique transcripts. The traversal is 
 guided by the initial RNAs to avoid a combinatorial explosion in alternative 
 splicing.
 <LI>Protein predictions are generated.
 </OL>
 
 <H2>Credits</H2>
 <P>
 The SIB Genes track was produced on the <A
 HREF="http://www.vital-it.ch" TARGET = _BLANK>Vital-IT</A> high-performance 
 computing platform
 using a computational pipeline developed by Christian Iseli with help from
 colleagues at the <A HREF="http://www.licr.org" TARGET = _BLANK>Ludwig institute 
 for Cancer
 Research</A> and the <A HREF="http://www.isb-sib.ch" TARGET = _BLANK>Swiss Institute 
 of Bioinformatics</A>.  It is based on data from NCBI <A
 HREF="http://www.ncbi.nlm.nih.gov/RefSeq/" TARGET=_blank>RefSeq</A> and <A
 HREF="http://www.ncbi.nlm.nih.gov/Genbank/index.html"
 TARGET=_blank>GenBank</A>/<A HREF="http://www.ebi.ac.uk/embl/" 
 TARGET = _BLANK>EMBL</A>.  Our
 thanks to the people running these databases and to the scientists worldwide
 who have made contributions to them. </P>
 
 <H2>References</H2>
 <P>
 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J,
 Wheeler DL. 
-<A HREF="http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D23" 
+<A HREF="http://nar.oupjournals.org/cgi/content/abstract/32/suppl_1/D23" 
 TARGET=_blank>GenBank: update</A>. 
 <em>Nucleic Acids Res.</em> 2004 Jan 1;32:D23-6.</P>