X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=e1b00c4d8cc42b2cac8f7202446613fce070e204;hb=refs%2Fheads%2Fbug%2FJAL-2210_hack_for_Release_2_10;hp=d124cc8d5de3e7904164dc87fd7fd9e7f48271db;hpb=9a881df532ecf49063d4f032144533b9a1a89319;p=jalview.git

diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
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+++ b/help/html/whatsNew.html
@@ -27,60 +27,47 @@
     <strong>What's new ?</strong>
   </p>
   <p>
-    Jalview 2.9 has been in development since December 2014. In addition
-    to a multitude of bug fixes and minor improvements (both small, and
-    rather big!), it also brings major new capabilities for codon-level
-    analysis of protein alignments and the manipulation of structural
-    data.<br />For the full list of changes, see the <a
-      href="releases.html#Jalview.2.9">Jalview 2.9 Release Notes</a>.
+    Jalview 2.10 is the next major release in the Jalview 2 series. Full
+    details are in the <a href="releases.html#Jalview.2.10.0">Jalview
+      2.10 Release Notes</a>, but the highlights are below.
   </p>
   <p>
-    <strong>Highlights in Jalview 2.9</strong>
-  
+    <strong>Highlights in Jalview 2.10</strong>
   <ul>
-    <li><strong>Visualisation, editing and analysis of
-        cDNA and Protein alignments</strong><br />A new <a
-      href="features/splitView.html">Split View</a> window allows linked
-      protein and nucleotide sequence alignments to be viewed, edited,
-      and analysed as one. <br />cDNA alignments can also be
-      reconstructed from protein alignments calculated by Jalview's web
-      services, and update in response to edits in the amino acid view.<br />To
-      start experimenting with cDNA/Protein analysis, jut drop a file
-      containing cDNA sequences which code for, and have IDs matching
-      proteins in an existing alignment, and Jalview will do the rest.</li>
-    <li><strong>Enhanced Integration of UCSF Chimera</strong> <br>Jalview
-      2.9 provides full support for the use of Chimera to view 3D
-      structures linked to alignment views in the Jalview Desktop. We've
-      also included support for saving Chimera sessions in Jalview
-      project files.<br />Jalview and Chimera communicate using local
-      web server connections, which may cause firewall alerts on some
-      systems, but has the advantage of allowing bidirectional
-      communication. Communication between Jalview and Chimera is now
-      much more responsive, and selected regions in Chimera are now
-      shown as highlighted regions in the Jalview desktop.</li>
-    <li><strong>Interactive querying of the PDBe</strong><br />Jalview
-      users can now browse and retrieve 3D structure data from the PDB
-      via the <a href="http://www.ebi.ac.uk/pdbe/api/doc/search.html">PDBe
-        Search API</a> (<a href="http://dx.doi.org/10.1093%2Fnar%2Fgkt1180">Gutmanas
-        et al 2014</a>). Developed in collaboration with the PDBe group at
-      EMBL-EBI, the interface allows both structured and free-text
-      queries to be performed, and allows automatic selection of the
-      most relevant structures for an alignment acording to a variety of
-      criteria.</li>
-    <li><strong>Improved support for RNA visualisation</strong><br />Jalview
-      2.9 integrates the latest version of the <a
-      href="http://varna.lri.fr">VARNA RNA Viewer</a>, and VARNA views
-      can also now be stored in Jalview projects. We've also dealt with
-      a number of lingering bugs in the VARNA/Jalview interface,
-      including the loss of pseudoknots when RNA secondary structure is
-      shown VARNA.</li>
-    <li><strong>Protein Secondary Structure predictions
-        with JPred4</strong>Jalview includes a number of new features for working
-      with secondary structure predictions from the JPred4 server. These
-      include the ability to automatically hide insertions and highlight
-      mutations in an alignment with respect to a reference sequence.
-      Jalview 2.9's new scrollable SVG HTML export mode was also
-      developed specifically for the JPred4 server.</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 <a href="features/siftsmapping.html">match structures
+            to UniProt sequences</a>, 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 <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
+      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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