8c2f7318d8d821de9b2a25750586a94ab5e8c1bb
lrnassar
  Fri Nov 15 18:50:19 2024 -0800
Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM.

diff --git src/hg/makeDb/trackDb/human/encodeGencodeGeneOct.html src/hg/makeDb/trackDb/human/encodeGencodeGeneOct.html
index 9bede4a..2304e3a 100755
--- src/hg/makeDb/trackDb/human/encodeGencodeGeneOct.html
+++ src/hg/makeDb/trackDb/human/encodeGencodeGeneOct.html
@@ -75,31 +75,31 @@
 <TR>
   <TD>Unprocessed_pseudogene</TD>
   <TD><FONT COLOR=005BBF> blue</FONT></TD>
   <TD>Pseudogenes arising via gene duplication (exon structure of parent gene retained)</TD>
 </TR>
 <TR>
   <TD>Artifact</TD>
   <TD><FONT COLOR=#636863>grey</FONT></TD>
   <TD>Transcript evidence and/or its translation equivocal</TD>
 </TR>
 </TABLE></P>
 
 <H2>Methods</H2>
 <P>
 The Human and Vertebrate Analysis and Annotation manual curation process 
-(<A HREF="http://www.sanger.ac.uk/HGP/havana/" TARGET=_blank>HAVANA</A>) was
+(<A HREF="https://www.sanger.ac.uk/HGP/havana/" TARGET=_blank>HAVANA</A>) was
 used to produce these annotations.
 <P>
 Finished genomic sequence was analyzed on a clone-by-clone basis using a
 combination of similarity searches against DNA and protein databases, as
 well as a series of <em>ab initio</em> gene predictions. Nucleotide sequence 
 databases were searched with WUBLASTN and significant hits were realigned
 to the unmasked genomic sequence by EST2GENOME. WUBLASTX was used to search 
 the Uniprot protein database, and the accession numbers of significant hits 
 were retrieved from the Pfam database. Hidden Markov models for Pfam protein 
 domains were aligned against the genomic sequence using Genewise to provide
 annotation of protein domains. 
 <P>
 A number of <em>ab initio</em>
 prediction algorithms were also run: Genscan and Fgenesh for genes, tRNAscan 
 to find tRNA genes, and Eponine TSS for transcription start site predictions.