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
@@ -17,31 +17,31 @@
 <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