src/hg/makeDb/trackDb/ccdsGene.html 1.9

Index: src/hg/makeDb/trackDb/ccdsGene.html
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RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/ccdsGene.html,v
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retrieving revision 1.9
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 <H2>Description</H2>
 <P>
 This track shows $organism genome high-confidence gene annotations from the
 <A HREF="http://www.ncbi.nlm.nih.gov/CCDS/" TARGET=_blank>Consensus 
 Coding Sequence (CCDS) project</A>. This project is a collaborative effort 
 to identify a core set of 
 $organism protein-coding regions that are consistently annotated and of high 
 quality. The long-term goal is to support convergence towards a standard set 
 of gene annotations on the $organism genome.
 </P>
 <P>Collaborators include:
 <UL>
 <LI><A HREF="http://www.ebi.ac.uk/" TARGET=_blank>European Bioinformatics 
 Institute</A> (EBI)
 <LI><A HREF="http://www.ncbi.nlm.nih.gov" TARGET=_blank>National Center for 
 Biotechnology Information</A> (NCBI)
 <LI><A HREF="http://www.cbse.ucsc.edu/" TARGET=_blank>University of 
 California, Santa Cruz</A> (UCSC)
 <LI><A HREF="http://www.sanger.ac.uk/" TARGET=_blank>Wellcome Trust Sanger 
 Institute</A> (WTSI)
 </UL>
 
 <H2>Methods</H2>
 <P>
 CDS annotations of the $organism genome were obtained from two sources:
 <A HREF="http://www.ncbi.nlm.nih.gov/RefSeq/index.html" TARGET=_blank>NCBI 
 RefSeq</A> and a union of the gene annotations from 
 <A HREF="http://www.ensembl.org/" TARGET=_blank>Ensembl</A> and 
 <A HREF="http://vega.sanger.ac.uk/" TARGET=_blank>Vega</A>, collectively known 
 as <EM>Hinxton</EM>.</P>
 <P>
 Genes with identical CDS genomic coordinates in both sets become CCDS 
 candidates. The genes undergo a quality evaluation, which must be approved by 
 all collaborators. The following criteria are currently used to assess each
 gene: 
 <UL>
 <LI> an initiating ATG, a valid stop codon, and no in-frame stop codons
 <LI> ability to be translated from the genome reference sequence without frameshifts
 <LI> recognizable splicing sites
 <LI> no intersection with putative pseudogene predictions
 <LI> supporting transcripts and protein homology
 <LI> conservation evidence with other species
 </UL></P>
 <P>
 A unique CCDS ID is assigned to the CCDS, which links together all gene 
 annotations with the same CDS.  CCDS gene annotations are under continuous
 review, with periodic updates to this track.
 </P>
 
 <H2>Credits</H2>
 <P>
 This track was produced at UCSC from data downloaded from the
 <A HREF="http://www.ncbi.nlm.nih.gov/CCDS/" TARGET=_blank>CCDS project</A> 
 web site.
 </P>
 
 <H2>References</H2>
 <P>
+Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, 
+Farrell CM, Loveland JE, Ruef BJ <EM>et al</EM>. 
+<A HREF="http://genome.cshlp.org/content/early/2009/06/04/gr.080531.108.long"
+TARGET=_blank>The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes</A>. 
+<I>Genome Res.</I> 2009 Jun 4. [Epub ahead of print]
+<P>
 Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, <EM>et al</EM>.
 <A HREF="http://nar.oupjournals.org/cgi/content/abstract/30/1/38" 
 TARGET=_blank>The Ensembl genome database project</A>. 
 <I>Nucl. Acids Res.</I> 2002 Jan 1;30(1):38-41.</P>
 <P>
 Pruitt KD, Tatusova T, Maglott DR.
 <A HREF="http://nar.oupjournals.org/cgi/content/full/33/suppl_1/D501" 
 TARGET=_blank>NCBI Reference Sequence (RefSeq): a curated non-redundant 
 sequence database of genomes, transcripts and proteins</A>. 
 <I>Nucl. Acids Res.</I> 2005 Jan 1;33(Database Issue):D501-D504. 
 </P>