From 84fee8925c31c432471ddc8a54c17b4ffaa9df64 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 19 Sep 2016 17:40:56 +0100
Subject: [PATCH] =?utf8?q?JAL-2189=20what=E2=80=99s=20new=20-=20ensembl,=20n?=
 =?utf8?q?ew=20structure=20stuff,=20reference=20seqs?=
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   <p>
     <strong>Highlights in Jalview 2.10</strong>
   <ul>
-    <li><strong>Ensembl sequence fetcher.</strong> Annotated Genes, transcripts and
-      proteins can be retrieved via Jalview's new Ensembl REST client.</li>
-    <li><strong>Improved sequence/structure mappings.</strong>
-      Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI) to
-      match PDB data positions in UniProt sequences.</li>
+    <li><strong>Ensembl sequence fetcher.</strong> Annotated Genes,
+      transcripts and proteins can be retrieved via Jalview's new <a
+      href="features/ensemblsequencefetcher.html">Ensembl REST
+        client</a>. Support for import of Ensembl data also allows:
+      <ul>
+        <li><strong>Sequence variant data.</strong> Jalview
+          propagates variant annotation imported via Ensembl onto
+          protein products, complete with associated metadata such as
+          clinical significance.</li>
+        <li><strong>Aligned locus view.</strong> Transcripts
+          retrieved for a gene identifier via the Ensembl or
+          EnsemblGenomes sequence databases are automatically aligned to
+          their reference genome.</li>
+      </ul></li>
+    <li><strong>Working with structures.</strong>
+      <ul>
+        <li><strong>More accurate structure mappings.</strong>
+          Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI)
+          to match structures to UniProt sequences, even for structures
+          containing multiple copies of a sequence.</li>
+        <li><strong>Import structures as mmCIF</strong>. Jalview
+          now downloads data from the EMBL-EBI's PDBe site as mmCIF.
+          mmCIF files allow Jalview to handle very large structures,
+          such as the HIV virus capsid assembly.</li>
+      </ul></li>
+    <li><strong>UniProt Free Text Search</strong>. The new search
+      dialog for UniProt allows you to browse and retrieve sequences
+      from UniProt with free-text search and more structured queries</li>
+    <li><strong>Reference sequence based alignment
+        visualisation.</strong>. When a reference sequence is defined for the
+      alignment, the alignment column ruler is now numbered according to
+      the reference sequence. The reference sequence for alignment views
+      can also be saved and restored from Jalview projects.</li>
+    <li></li>
   </ul>
 
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