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/human/affyHuEx1.html src/hg/makeDb/trackDb/human/affyHuEx1.html
index 6bdea49eb03..b022183c7b6 100644
--- src/hg/makeDb/trackDb/human/affyHuEx1.html
+++ src/hg/makeDb/trackDb/human/affyHuEx1.html
@@ -1,18 +1,18 @@
 <H2>Description</H2>
 <P>
-The <A HREF="http://www.affymetrix.com/estore/browse/products.jsp?navMode=
+The <A HREF="https://www.affymetrix.com/estore/browse/products.jsp?navMode=
 34000&productId=131452&navAction=jump&aId=productsNav#1_1"
 TARGET=_blank>Human Exon 1.0 ST</A> GeneChip contains over 1.4 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 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,
@@ -32,40 +32,40 @@
 on the <B>Affy All Exon</B> track.</P>
 
 <H2>Credits and References</H2>
 <P>
 The exons interrogated by the probe sets displayed in this track are
 from the Affymetrix Human 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/index.html" 
 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 Research</em>. 2002 Jan 1;30(1):38-41.</P>
 <P>
 <B>Exoniphy:</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., Guigo, R. 
 <A HREF="https://genome.cshlp.org/content/10/4/511.abstract"
 TARGET=_blank>Geneid in Drosophila</A>.
 <em>Genome Res.</em> <B>10</B>(4), 511-515 (2000).</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>.