JAL-2189 release notes

[jalview.git] / help / html / whatsNew.html

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index e1b00c4..1743f1c 100755 (executable)
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -37,16 +37,16 @@
     <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:
+        client</a>. Support for import of Ensembl data allows:
       <ul>
         <li><strong>Sequence variant data.</strong> Jalview
-          propagates variant annotation imported via Ensembl onto
+          propagates variant annotation on genomic regions onto transcripts and
           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>
+          their reference genome, and introns hidden from the view.</li>
       </ul></li>
     <li><strong>Working with structures.</strong>
       <ul>
@@ -59,15 +59,19 @@
           now downloads data from the EMBL-EBI's PDBe site as <a href="features/mmcif.html">mmCIF</a>.
           This allows very large structures to be imported, such as the HIV virus capsid assembly.</li>
       </ul></li>
-    <li><strong>UniProt Free Text Search</strong>. The new search
+    <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>
+    <li><strong>Reference sequence alignment view.</strong>.
+      Jalview 2.9 introduced support for reference sequences. In 2.10,
+      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><strong>Ensembl and ENA 'show cross-references'
+        support.</strong>The Calculations menu's 'Show cross-references' will now
+      offer Ensembl as well as EMBLCDS and Uniprot when CDS/Protein
+      mapping data is available for download or display.</li>
   </ul>
 
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