19870454d7c3d8f29a5800477bcaa36babee5a98
dschmelt
  Tue Nov 2 17:10:33 2021 -0700
Finishing Development for jaspar update refs #28322

diff --git src/hg/makeDb/trackDb/human/jaspar.html src/hg/makeDb/trackDb/human/jaspar.html
index aca3fcd..e65cf56 100644
--- src/hg/makeDb/trackDb/human/jaspar.html
+++ src/hg/makeDb/trackDb/human/jaspar.html
@@ -1,20 +1,20 @@
 <h2>Description</h2>
 <p>
 This track represents genome-wide predicted binding sites for TF 
 (transcription factor) binding profiles in the 
-<a href="https://jaspar.genereg.net//about/" target="_blank">JASPAR 
+<a href="https://jaspar.genereg.net/about/" target="_blank">JASPAR 
 CORE collection</a>. This open-source database contains a curated, non-redundant 
 set of binding profiles derived from published collections of experimentally 
 defined transcription factor binding sites for eukaryotes.</p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
 Shaded boxes represent predicted binding sites for each of the TF profiles
 in the JASPAR CORE collection. The shading of the boxes indicates 
 the p-value of the profile's match to that position (scaled between 
 0-1000 scores, where 0 corresponds to a p-value of 1 and 1000 to a 
 p-value &le; 10<sup>-10</sup>). Thus, the darker the shade, the 
 lower (better) the p-value.</p>
 
 <p>
 The default view only shows predicted binding sites with scores of 400 or greater. 
@@ -79,33 +79,34 @@
     <td style="padding:10px">0.049</td>
     <td style="padding:10px">10<sup>-2</sup></td>
     <td style="padding:10px">10<sup>-3</sup></td>
     <td style="padding:10px">10<sup>-4</sup></td>
     <td style="padding:10px">10<sup>-5</sup></td>
     <td style="padding:10px">10<sup>-6</sup></td>
     <td style="padding:10px">10<sup>-7</sup></td>
     <td style="padding:10px">10<sup>-8</sup></td>
     <td style="padding:10px">10<sup>-9</sup></td>
     <td style="padding:10px">&le; 10<sup>-10</sup></td>
   </tr>
 </table>
 
 <h2>Methods</h2>
 <p>
-JASPAR 2022 contains updates transcription factor binding sites
+JASPAR 2022 contains updated transcription factor binding sites
 with additional transcription factor profiles. More information on
-the methods can be found in the upcoming publication.</p>
+the methods can be found in their upcoming publication or on the
+<a href="https://jaspar.genereg.net/" target="_blank">JASPAR website</a>.</p>
 
 <p>
 JASPAR 2020 scanned DNA sequences with JASPAR CORE TF-binding profiles 
 for each taxa independently using PWMScan. TFBS predictions were selected with 
 a PWM relative score &ge; 0.8 and a p-value &lt; 0.05. P-values were scaled 
 between 0 (corresponding to a p-value of 1) and 1000 (p-value &le; 10<sup>-10</sup>) for 
 colouring of the genome tracks and to allow for comparison of prediction 
 confidence between different profiles.</p>
 
 <p> 
 JASPAR 2018 used the TFBS Perl module (Lenhard and Wasserman 2002) 
 and FIMO (Grant, Bailey, and Noble 2011), as distributed within the MEME suite 
 (version 4.11.2) (Bailey <em>et al.</em> 2009). For scanning genomes with the 
 BioPerl TFBS module, profiles were converted to PWMs and matches were kept with a 
 relative score &ge; 0.8. For the FIMO scan, profiles were reformatted to MEME motifs 
@@ -152,33 +153,32 @@
 <a href="../cgi-bin/hgHubConnect?hubSearchTerms=jaspar&hgHub_do_search=on">
 Public Hub</a> or by clicking the assembly links below:</p>
 <table width="458" border="1">
   <tbody>
     <tr>
       <td><strong>Species</strong></td>
       <td><strong>Genome assembly versions</strong></td>
     </tr>
     <tr>
       <td width="300">Human - <em>Homo sapiens</em></td>
       <td width="200"><a target="_blank" href="../cgi-bin/hgTrackUi?db=hg19&g=jaspar">hg19</a>, 
 <a target="_blank" href="../cgi-bin/hgTrackUi?db=hg38&g=jaspar">hg38</a></td>
     </tr>
     <tr>
       <td>Mouse - <em>Mus musculus</em></td>
-      <td><a target="_blank" 
-href="../cgi-bin/hgTracks?db=mm10&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">
-mm10</a></td>
+      <td><a target="_blank" href="../cgi-bin/hgTrackUi?db=mm10&g=jaspar">mm10</a>, 
+<a target="_blank" href="../cgi-bin/hgTrackUi?db=mm39&g=jaspar">mm39</a></td>
     </tr>
     <tr>
       <td>Zebrafish - <em>Danio rerio</em></td>
       <td><a target="_blank" 
 href="../cgi-bin/hgTracks?db=danRer11&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">danRer11</a></td>
     </tr>
     <tr>
       <td>Fruitfly - <em>Drosophila melanogaster</em></td>
       <td><a target="_blank" 
 href="../cgi-bin/hgTracks?db=dm6&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">dm6</a></td>
     </tr>
     <tr>
       <td>Nematode - <em>Caenorhabditis elegans</em></td>
       <td><a target="_blank" 
 href="../cgi-bin/hgTracks?db=ce10&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt">ce10</a></td>