089c09e98db52e92da694ab1a0c8891c1a7fd3e8 gperez2 Thu Apr 2 15:50:07 2026 -0700 Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM. diff --git src/hg/makeDb/trackDb/ccdsGene.html src/hg/makeDb/trackDb/ccdsGene.html index c6d4eb022b7..31b8c759d19 100644 --- src/hg/makeDb/trackDb/ccdsGene.html +++ src/hg/makeDb/trackDb/ccdsGene.html @@ -1,94 +1,94 @@ <H2>Description</H2> <P> This track shows $organism genome high-confidence gene annotations from the <A HREF="https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi" 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="https://www.ebi.ac.uk/" TARGET=_blank>European Bioinformatics Institute</A> (EBI) <LI><A HREF="https://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="https://www.sanger.ac.uk/" TARGET=_blank>Wellcome Trust Sanger Institute</A> (WTSI) </UL> <p> For more information on the different gene tracks, see our <a target=_blank href="/FAQ/FAQgenes.html">Genes FAQ</a>.</p> <H2>Methods</H2> <P> CDS annotations of the $organism genome were obtained from two sources: <A HREF="https://www.ncbi.nlm.nih.gov/refseq/" TARGET=_blank>NCBI RefSeq</A> and a union of the gene annotations from -<A HREF="http://www.ensembl.org/index.html" TARGET=_blank>Ensembl</A> and +<A HREF="https://www.ensembl.org/index.html" TARGET=_blank>Ensembl</A> and <A HREF="http://vega.archive.ensembl.org/index.html" 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 (Exception: a non-ATG translation start codon is annotated if it has sufficient experimental support), a valid stop codon, and no in-frame stop codons (Exception: selenoproteins, which contain a TGA codon that is known to be translated to a selenocysteine instead of functioning as a stop codon) <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="https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi" TARGET=_blank>CCDS project</A> web site. </P> <H2>References</H2> <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="https://academic.oup.com/nar/article/30/1/38/1332872/The-Ensembl-genome-database-project" target="_blank">The Ensembl genome database project</a>. <em>Nucleic Acids Res</em>. 2002 Jan 1;30(1):38-41. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11752248" target="_blank">11752248</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC99161/" target="_blank">PMC99161</a> </p> <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="https://genome.cshlp.org/content/19/7/1316.long" target="_blank"> The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes</a>. <em>Genome Res</em>. 2009 Jul;19(7):1316-23. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19498102" target="_blank">19498102</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2704439/" target="_blank">PMC2704439</a> </p> <p> Pruitt KD, Tatusova T, Maglott DR. <a href="https://academic.oup.com/nar/article/33/suppl_1/D501/2505241/NCBI-Reference-Sequence- RefSeq-a-curated-non" target="_blank"> NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins</a>. <em>Nucleic Acids Res</em>. 2005 Jan 1;33(Database issue):D501-4. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15608248" target="_blank">15608248</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539979/" target="_blank">PMC539979</a> </p>