cdf97b3df98fc12b2b58df8c44a1b0e532fc27de
jnavarr5
  Tue May 12 15:52:55 2020 -0700
Updating http to https for panTro2, uiLinks cronjob.

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 <H2>Description</H2>
 <P>
 This track shows gene predictions using the N-SCAN gene structure prediction
 software provided by the Computational Genomics Lab at Washington University 
 in St. Louis, MO, USA.
 </P>
 
 <H2>Methods</H2>
 <P>
 N-SCAN combines biological-signal modeling in the target genome sequence along
 with information from a multiple-genome alignment to generate de novo gene
 predictions. It extends the TWINSCAN target-informant genome pair to allow for
 an arbitrary number of informant sequences as well as richer models of
 sequence evolution. N-SCAN models the phylogenetic relationships between the
 aligned genome sequences, context-dependent substitution rates, insertions,
 and deletions.
 </P>
 <P>${informant}</P>
 
 <H2>Credits</H2>
 <P>
-Thanks to <A HREF="http://mblab.wustl.edu/" 
+Thanks to <A HREF="https://mblab.wustl.edu/" 
 TARGET=_blank>Michael Brent's Computational Genomics Group</A> at Washington 
 University St. Louis for providing this data.
 </P>
 <p>
 Special thanks for this implementation of N-SCAN to Aaron Tenney in
 the Brent lab, and Robert Zimmermann, currently at Max F. Perutz
 Laboratories in Vienna, Austria.
 </p>
 
 <H2>References</H2>
 <p>
 Gross SS, Brent MR.
 <a href="https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.379" target="_blank">
 Using multiple alignments to improve gene prediction</a>.
 <em>J Comput Biol</em>. 2006 Mar;13(2):379-93.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16597247" target="_blank">16597247</a>
 </p>
 
 <P>
 Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM,
 Rusch DB, Town CD <EM>et al</EM>.
 <a href="https://academic.oup.com/nar/article/31/19/5654/1092988/Improving-the-Arabidopsis-genome-annotation-using"
 target="_blank">Improving the <EM>Arabidopsis</EM> genome annotation using maximal transcript 
 alignment assemblies</A>.
 <em>Nucleic Acids Res</em>. 2003 Oct 1;31(19):5654-66.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500829" target="_blank">14500829</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC206470/" target="_blank">PMC206470</a>
 </p>
 
 <P>
 Korf I, Flicek P, Duan D, Brent MR.
 <A HREF="https://academic.oup.com/bioinformatics/article/17/suppl_1/S140/261903/Integrating-genomic-homology-into-gene-structure"
 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>
 van Baren MJ, Brent MR.
 <A HREF="https://genome.cshlp.org/content/16/5/678.abstract"
 TARGET=_blank>Iterative gene prediction and pseudogene removal improves
 genome annotation</A>.
 <em>Genome Res</em>. 2006 May;16(5):678-85.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16651666" target="_blank">16651666</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1457044/" target="_blank">PMC1457044</a>
 </p>