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/affyAllExonProbes.html src/hg/makeDb/trackDb/affyAllExonProbes.html
index f7fdf022fe6..d11eb6b24ed 100644
--- src/hg/makeDb/trackDb/affyAllExonProbes.html
+++ src/hg/makeDb/trackDb/affyAllExonProbes.html
@@ -1,138 +1,138 @@
 <H2>Description</H2>
 <P>
 The <A HREF="https://www.affymetrix.com:443/estore/products_services/arrays/index.affx"
 TARGET=_blank>Exon GeneChip</A> contains over one million probe 
 sets
 designed to interrogate individual exons rather than the 3' ends of transcripts
 as in traditional GeneChips. Exons were derived from a variety of
 annotations that have been divided into the classes Core, Extended
 and Full. 
 <UL> 
   <LI><B>Core:
     </B>RefSeq transcripts, full-length GenBank mRNAs</LI>
   <LI><B>Extended:</B> 
     dbEst alignments, Ensembl annotations, syntenic mRNA from human, rat and mouse, 
     microRNA annotations, MITOMAP annotations, Vega genes, Vega pseudogenes
   <LI><B>Full:</B>
     Geneid genes, Genscan genes, Genscan Subopt, Exoniphy, RNA genes, SGP genes,
     Twinscan genes
   </LI>
 </UL></P> 
 
 <P>
 Probe sets are colored by class with the Core probe sets being
 the darkest and the Full being the lightest color. Additionally, probe
 sets that do not overlap the exons of a transcript cluster, but fall
 inside of its introns, are considered bounded by that transcript
 cluster and are colored slightly lighter. Probe sets that overlap the
 coding portion of the Core class are colored slightly darker.</P>
 <P>
 The microarray track using this probe set can be displayed by turning
 on the <B>Affy Exon Tissue</B> track.</P>
 
 <H2>Credits and References</H2>
 <P>
 The exons interrogated by the probe sets displayed in this track are
 from the Affymetrix Exon 1.0 GeneChip and were derived from a
 number of sources. In addition to the millions of cDNA sequences
 contributed to the 
 <A HREF="https://www.ncbi.nlm.nih.gov/genbank/" 
 TARGET=_blank>GenBank</A>, 
 <A HREF="https://www.ncbi.nlm.nih.gov/dbEST/" TARGET=_blank>dbEst</A> and 
 <A HREF="https://www.ncbi.nlm.nih.gov/refseq/" TARGET=_blank>RefSeq</A> 
 databases by
 individual labs and scientists, the following annotations were used:
 <P>
-<A HREF="http://www.ensembl.org/index.html" 
+<A HREF="https://www.ensembl.org/index.html" 
 TARGET=_blank><B>Ensembl</B></A><B>: </B>
 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" 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>
 <a href="http://compgen.cshl.edu/phast/" target"_blank"><B>Exoniphy</a>:</B> Siepel, A., Haussler, D. 
-<A HREF="http://compgen.cshl.edu/~acs/recomb2004.pdf"
+<A HREF="https://doi.org/10.1101/gr.3715005"
 TARGET=_blank>Computational identification of evolutionarily conserved 
 exons</A>.
 <em>Proc. 8th Int'l Conf. on Research in Computational Molecular Biology</em>, 
 177-186 (2004).
 </P>
 
 <P>
 <B><A HREF="https://genome.crg.es/geneid.html" TARGET=_blank>Geneid Genes</A>:</B>
 Parra G, Blanco E, Guig&#243; R.
 <a href="https://genome.cshlp.org/content/10/4/511.abstract" target="_blank">
 GeneID in Drosophila</a>.
 <em>Genome Res</em>. 2000 Apr;10(4):511-5.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/10779490" target="_blank">10779490</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC310871/" target="_blank">PMC310871</a>
 </p>
 
 <P>
 <B><A HREF="http://hollywood.mit.edu/GENSCAN.html" TARGET=_blank>Genscan Genes</A>:</B> 
 Burge C, Karlin S.
 <a href="https://www.sciencedirect.com/science/article/pii/S0022283697909517" target="_blank">
 Prediction of complete gene structures in human genomic DNA</a>.
 <em>J Mol Biol</em>. 1997 Apr 25;268(1):78-94.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/9149143" target="_blank">9149143</a>
 </p>
 
 <P>
 <B><A HREF="https://www.mirbase.org/" TARGET=_blank>microRNA</A>:</B>
 Griffiths-Jones S.
 <a href="https://academic.oup.com/nar/article/32/suppl_1/D109/2505171" target="_blank">
 The microRNA Registry</a>.
 <em>Nucleic Acids Res</em>. 2004 Jan 1;32(Database issue):D109-11.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14681370" target="_blank">14681370</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC308757/" target="_blank">PMC308757</a>
 </p>
 
 <P>
 <B><A HREF="https://www.mitomap.org//MITOMAP" TARGET=_blank>MITOMAP</A>:</B>
 Kogelnik AM, Lott MT, Brown MD, Navathe SB, Wallace DC.
 <a href="https://academic.oup.com/nar/article/33/suppl_1/D611/2505354" target="_blank">
 MITOMAP: a human mitochondrial genome database</a>.
 <em>Nucleic Acids Res</em>. 1996 Jan 1;24(1):177-9.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/8594574" target="_blank">8594574</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC145607/" target="_blank">PMC145607</a>
 </p>
 
 <P>
 <B><A HREF="http://eddylab.org" TARGET=_blank>RNA Genes</A>:</B>
 Lowe TM, Eddy SR.
 <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC146525/pdf/250955.pdf" target="_blank">
 tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence</a>.
 <em>Nucleic Acids Res</em>. 1997 Mar 1;25(5):955-64.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/9023104" target="_blank">9023104</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC146525/" target="_blank">PMC146525</a>
 </p>
 
 <P>
 <B><A HREF="https://grib.upf.edu/" TARGET=_blank>SGP Genes</A>: </B> 
 Wiehe T, Gebauer-Jung S, Mitchell-Olds T, Guig&#243; R.
 <a href="https://genome.cshlp.org/content/11/9/1574.full" target="_blank">
 SGP-1: prediction and validation of homologous genes based on sequence alignments</a>.
 <em>Genome Res</em>. 2001 Sep;11(9):1574-83.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11544202" target="_blank">11544202</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC311140/" target="_blank">PMC311140</a>
 </p>
 
 <P>
 <B><A HREF="https://mblab.wustl.edu/" TARGET=_blank>Twinscan Genes</A>:</B>
 Korf I, Flicek P, Duan D, Brent MR.
 <a href="https://academic.oup.com/bioinformatics/article/17/suppl_1/S140/261903" target="_blank">
 Integrating genomic homology into gene structure prediction</a>.
 <em>Bioinformatics</em>. 2001;17 Suppl 1:S140-8.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11473003" target="_blank">11473003</a>
 </p>
 
 <P>
 <B><A HREF="http://vega.archive.ensembl.org/index.html" TARGET=_blank>Vega Genes 
 and Pseudogenes</A>: </B>The HAVANA group, 
 <A HREF="https://www.sanger.ac.uk/" TARGET=_blank>Wellcome Trust Sanger 
 Institute</A>.</P>