</head>
<body>
<p>
- <strong>What's new ?</strong>
+ <strong>What's new in Jalview 2.10.3b1 ?</strong>
</p>
<p>
- 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.
+ This release - Jalview 2.10.3b1 is the January 2018 patch release for Version 2.10.3 was released in November 2017. The major focus was to
+ improve Jalview's sequence features datamodel and the scalability of
+ the alignment rendering system. The bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.3b1">2.10.3b1
+ Release Notes</a>.
</p>
+ <p>The highlights for Jalview 2.10.3 include:
+ </p>
+ <ul>
+ <li>Faster and more responsive UI when importing and working
+ with wide alignments and handling hundreds and thousands of
+ sequence features</li>
+ <li>Improved usability with <a
+ href="features/pdbsequencefetcher.html">PDB</a> and <a
+ href="features/uniprotsequencefetcher.html">UniProt</a> Free Text
+ Search dialog, and new tab for retrieval of sequences for lists of
+ IDs.
+ </li>
+ <li>Short names assigned to sequences retrieved from UniProt</li>
+ <li>Groovy console upgraded to 2.4.12 (improved support for Java 9)</li>
+ </ul>
<p>
- <strong>Highlights in Jalview 2.10</strong>
+ <strong><a name="experimental">Experimental Features</a></strong>
+ </p>
+ <p>
+ Remember, please enable the <em>Experimental Features</em> option in
+ the Jalview Desktop's <em>Tools</em> menu, and then restart Jalview
+ if you want to try out features below:
+ </p>
<ul>
- <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 allows:
- <ul>
- <li><strong>Sequence variant data.</strong> Jalview
- 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, and introns hidden from the view.</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 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>
+ <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
+ <a href="features/chimera.html#experimental">new entries in
+ the Chimera viewer's Chimera menu</a> allow positional annotation to
+ be exchanged between Chimera and Jalview.</li>
</ul>
-
+
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff