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/sibGene.html src/hg/makeDb/trackDb/sibGene.html
index c02cd82..0b3b4d9 100644
--- src/hg/makeDb/trackDb/sibGene.html
+++ src/hg/makeDb/trackDb/sibGene.html
@@ -1,49 +1,49 @@
 <H2>Description</H2>
 <P>
 The SIB Genes track is a transcript-based set of gene predictions based
 on data from RefSeq and EMBL/GenBank. Genes all have the support of at
 least one GenBank full length RNA sequence, one RefSeq RNA, or one spliced
 EST.  The track includes both protein-coding and non-coding transcripts.
 The coding regions are predicted using
-<A HREF="http://estscan.sourceforge.net" TARGET="_BLANK">ESTScan</A>.</P>
+<A HREF="https://estscan.sourceforge.net/" TARGET="_BLANK">ESTScan</A>.</P>
 
 <H2>Display Conventions and Configuration</H2>
 <P>
 This track in general follows the display conventions for
 <A HREF="../goldenPath/help/hgTracksHelp.html#GeneDisplay">gene prediction
 tracks</A>.  The exons for putative non-coding genes and untranslated regions 
 are represented by relatively thin blocks while those for coding open 
 reading frames are thicker.</P>
 <P>
 This track contains an optional codon coloring
 feature that allows users to quickly validate and compare gene predictions.
 To display codon colors, select the <em>genomic codons</em> option from the
 <em>Color track by codons</em> pull-down menu.  Go to the
 <A HREF="../goldenPath/help/hgCodonColoring.html">Coloring Gene Predictions and
 Annotations by Codon</A> page for more information about this feature. </P>
 <P>Further information on the predicted transcripts can be found on the
 <A HREF="https://ccg.vital-it.ch/tromer/" TARGET="_BLANK">Transcriptome Web
 interface</A>.</P>
 
 
 <H2>Methods</H2>
 <P>
 The SIB Genes are built using a multi-step pipeline:  
 <OL>
 <LI>RefSeq and GenBank RNAs and ESTs are aligned to the genome with
-<A HREF="http://sibsim4.sourceforge.net" TARGET="_BLANK">SIBsim4</A>, keeping 
+<A HREF="https://sibsim4.sourceforge.net/" TARGET="_BLANK">SIBsim4</A>, keeping 
 only the best alignments for each RNA.
 <LI>Alignments are broken up at non-intronic gaps, with small isolated 
 fragments thrown out.
 <LI>A splicing graph is created for each set of overlapping alignments. This
 graph has an edge for each exon or intron, and a vertex for each splice site,
 start, and end.  Each RNA that contributes to an edge is kept as evidence for
 that edge.
 <LI>The graph is traversed to generate all unique transcripts. The traversal is 
 guided by the initial RNAs to avoid a combinatorial explosion in alternative 
 splicing.
 <LI>Protein predictions are generated.
 </OL>
 
 <H2>Credits</H2>
 <P>