src/hg/makeDb/trackDb/rnaCluster.html 1.13

Index: src/hg/makeDb/trackDb/rnaCluster.html
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RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/rnaCluster.html,v
retrieving revision 1.12
retrieving revision 1.13
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--- src/hg/makeDb/trackDb/rnaCluster.html	29 Aug 2007 23:06:19 -0000	1.12
+++ src/hg/makeDb/trackDb/rnaCluster.html	23 Jan 2010 00:53:44 -0000	1.13
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 <H2>Description</H2>
 <P>
 This track shows the boundaries of genes and the direction of
 transcription as deduced from clustering spliced ESTs and mRNAs
 against the genome.  When many spliced variants of the same gene exist, 
 this track shows the variant that spans the greatest distance in the 
 genome.</P>
 
 <H2>Method</H2>
 <P>
 ESTs and mRNAs from 
 <A HREF="http://www.ncbi.nlm.nih.gov/Genbank/index.html" 
 TARGET=_blank>GenBank</A> were aligned against the genome using blat.
 Alignments with less than 97.5% base identity within the aligning blocks 
 were filtered out. When multiple alignments occurred, only those
 alignments with a percentage identity within 0.2% of the
 best alignment were kept. The following alignments were also discarded: 
 ESTs that aligned without any introns, blocks smaller than 10 bases, and 
 blocks smaller than 130 bases that were not located next to an intron.  
 The orientations of the ESTs and mRNAs were deduced from the GT/AG splice 
 sites at the introns; ESTs and mRNAs with overlapping blocks
 on the same strand were merged into clusters.  Only the
 extent and orientation of the clusters are shown in this track.</P>
 <P>
 Scores for individual gene boundaries were assigned based on the number of 
 cDNA alignments used:
 <UL>
 <LI>300 &mdash; based on a single cDNA alignment<br> 
 <LI>600 &mdash; based on two alignments<br> 
 <LI>900 &mdash; based on three alignments<br>
 <LI>1000 &mdash; based on four or more alignments<br>
 </UL></P>
 
 <H2>Credits</H2>
 <P>
 This track, which was originally developed by Jim Kent,
 was generated at UCSC and uses data submitted to GenBank by 
 scientists worldwide.</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>
 <P>
 Kent WJ.
 <A HREF="http://www.genome.org/cgi/content/abstract/12/4/656"
 TARGET=_blank>BLAT - the BLAST-like alignment tool</A>.
 <em>Genome Res.</em> 2002 Apr;12(4):656-64.</P>