977f55b39381863017d7fb6d245b8d6c9e82cd57
lrnassar
  Wed Nov 29 11:20:11 2023 -0800
Adding documentation for searching previous NM accessions, refs #26016

diff --git src/hg/htdocs/goldenPath/help/query.html src/hg/htdocs/goldenPath/help/query.html
index 83cab8e..bace562 100755
--- src/hg/htdocs/goldenPath/help/query.html
+++ src/hg/htdocs/goldenPath/help/query.html
@@ -23,30 +23,32 @@
 <ul> 
   <li>
   Chromosome numbers</li> 
   <li>
   Chromosomal coordinate ranges</li> 
   <li>
   Gene names</li> 
   <li>
   Accession numbers</li> 
   <li>
   An mRNA, EST or STS marker</li> 
   <li>
   Keywords from the GenBank description of an mRNA</li> 
   <li>
   <a href="http://varnomen.hgvs.org/" target="_blank">HGVS</a> terms</li>
+  <li>
+  HGVS and accession searches on outdated RefSeq accession versions is available on hg38</li>
 </ul> 
 <p> 
 To specify a genome position:</p> 
 <ol> 
   <li>
   Select the desired clade, genome and assembly</li> 
   <li>
   Enter the desired query in the &quot;Position/Search Term&quot; box (see sample queries 
   below)</li> 
   <li>
   Click the &quot;Go&quot; button</li> 
 </ol> 
 <p> 
 Note: A query may have multiple results. If this is the case, a results page will appear listing 
 each result along with the track it is associated with. Once selected, the result will be displayed 
@@ -132,30 +134,34 @@
     refSeqs, SNPS, etc.</td></tr>
   <tr>
     <td>NR_026861.1:1-1000</td>
     <td>Works with any other type of accession from this page: Displays the first 1000bp of NR_026861.1</td></tr> 
   <tr id="HGVS">
     <td nowrap>NM_000310.4(PPT1):c.271_287del17insTT<br> NM_007262.5(PARK7):c.-24+75_-24+92dup<br>
     NM_006172.4(NPPA):c.456_*1delAA<br> MYH11:c.503-14_503-12del<br> 
     NM_198576.4(AGRN):c.1057C&gt;T<br> NM_198056.3:c.1654G&gt;T<br> NP_002993.1:p.Asp92Glu<br>
     NP_002993.1:p.D92E<br> BRCA1 Ala744Cys<br> BRCA1 A744C<br> LRG_100t1:c.4G>A<br> LRG_100t1:n.1<br>
     LRG_456p1:p.Ser190Leu<br>LRG_321:g.16409_16461del<br>ENST00000002596.6:c.-108-6848A&gt;G<br>
     ENSP00000005178.5:p.Val20Gly<br>
     chrX:g.31500000_31600000del<br> NR_111987:n.-1 <br> NM_015102.5:n.3038-2<br>
     NM_001372044:c.1528_1530del</td>
     <td>Displays the region that matches the <a href="http://varnomen.hgvs.org/" target="_blank">HGVS</a> 
         expression, usually in the format <tt>&lt;transcript or protein&gt;:&lt;position&gt; &lt;amino acid or nucleotide change&gt;</tt><br>If a gene symbol is used, HGVS search will try all RefSeq transcripts to find the nucleotide or amino acid at the position indicated in the expression. If there are multiple matches, a disambiguation page will be shown. If the RefSeq sequence differs from the genome sequence, then currently the search will use the genome, not the transcript, for codon counting and amino acid / nucleotide  comparison. Please contact us if this is inconvenient.</td></tr> 
+  <tr>
+    <td>NM_198056.2:c.1A&gt;C</td>
+    <td>An example of an HGVS search on a previous NM version that is now outdated. 
+        Support for previous NM accessions is only available on hg38.</td></tr>
 <!-- commented out -- not working 
   <tr> 
     <td>15q11;15q13</td>
     <td>bands 15q11 to 15q13, or SNPs rs1042522 and rs1800370. This syntax may also be used for 
     other range queries</td></tr> 
   <tr>
     <td>rs1042522;rs1800370</td> 
     <td>such as between uniquely determined ESTs, mRNAs, refSeqs, etc.</td></tr> 
 --> 
   <tr>
     <td>essv8694097</td>
     <td>Displays the region covering the copy number variant with the accession essv8694097 in the
         Database of Genomic Variants (DGV)</td></tr>
   <tr>
     <td>nssv3446126</td>