345a74e5374d0661c43bd619450ea34372f3931f
gperez2
  Tue Jan 31 10:50:49 2023 -0800
Updating news and pennantIcons for the hg38 patch 14 announcement, refs #29964

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         <li><a href="#2006">2006 News</a></li>
         <li><a href="#2005">2005 News</a></li>
         <li><a href="#2004">2004 News</a></li>
         <li><a href="#2003">2003 News</a></li>
         <li><a href="#2001">2001</a>-<a href="#2002">2002 News</a></li>
       </ul>
     </div>
   </div> 
 </div>
 
 <!-- ============= 2022 archived news ============= -->
 <p>You can sign-up to get these announcements via our 
 <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a>
 email list. We send around one short announcement email every two weeks.</p>
 
+<a name="2023"></a>
+
+<a name="013023"></a>
+<h2>Jan. 30, 2023 &nbsp;&nbsp; Addition of GRCh38 patch 14 sequences to hg38</h2>
+<p>
+We are pleased to announce the addition of GRCh38 patch release 14 to the
+<a href="../../cgi-bin/hgGateway?db=hg38">hg38</a> assembly. hg38 has been updated with patches
+since its release in 2013. The GRC patch releases do not change any previously existing
+sequences; they simply add new sequences for fix patches or alternate haplotypes that correspond
+to specific regions of the main chromosome sequences. For most users, the patches are unlikely
+to make a difference and may complicate the analysis as they introduce more duplication.</p>
+
+<p>
+More information on how patch sequences are incorporated can be found on the
+<a href="http://genome.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post.
+The blog post contains details about the new
+<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/latest/"
+target="_blank">/latest</a>,
+<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/initial/"
+target="_blank">/initial</a>, and
+<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/p14/" target="_blank">/p14</a>
+download directories on the downloads server. With the addition of new sequences to hg38, we can
+expect to see BLAT return more matches to the genome.</p>
+
+<ul>
+  <li>
+    The <b>initial/</b> subdirectory contains files for the initial release of GRCh38, which has 455
+    sequences, 261 alternate sequences, and no fix sequences. It is the same as the
+    parent download directory. This is probably the best genome file for aligners and most analysis
+    tasks, a version called &quot;analysisSet&quot; for the human genome.
+  </li>
+  <li>
+    The <b>p14/</b> subdirectory contains files for GRCh38.p14 (patch release 14), which has 711
+    sequences, 351 alternate sequences, and 166  fix sequences.
+  </li>
+  <li>
+    The <b>latest/</b> symbolic link points to the subdirectory for the most recent patch version.
+  </li>
+</ul>
+
+<p>
+We would like to thank the <a href="https://www.ncbi.nlm.nih.gov/grc" target="_blank">Genome
+Research Consortium</a> for creating the patches for hg38. We would also like to thank Galt Barber,
+Jairo Navarro, and Gerardo Perez at UCSC for implementing and testing the latest patch to the
+hg38 genome.</p>
+
 <a name="2022"></a>
 
 <a name="122022"></a>
 <h2>Dec 20, 2022 &nbsp;&nbsp; Multiz Alignment &amp; Conservation (470 mammals) for hg38</h2>
 <p>
 A new <a href="/cgi-bin/hgTrackUi?db=hg38&g=cons470way" target="_blank">470-way Multiz Alignment
 &amp; Conservation</a> track has been added to the human <a href="/cgi-bin/hgGateway?db=hg38"
 target="_blank">(GRCh38/hg38)</a> genome browser. The composite track displays multiple alignments
 (Multiz) and measurements of evolutionary conservation (phastCons and phyloP) for 470 mammals.
 </p>
 <h3>Tracks available:</h3>
 <ul>
     <li>Multiz Alignments of 470 mammals</li> 
     <li>470 mammals Basewise Conservation by PhyloP</li>
     <li>470 mammals Element Conservation by PhastCons</li>