</head>
<body>
<p>
- <strong>What's new in Jalview 2.10.0b1 ?</strong>
+ <strong>What's new in Jalview 2.10.3b1 ?</strong>
</p>
<p>
- Jalview 2.10.0b1 is a patch release for 2.10, the next major release
- in the Jalview 2 series. Full details are in the <a
- href="releases.html#Jalview.2.10.0b1">Jalview 2.10b1 Release
- Notes</a>, but the highlights are below.
+ This is the January 2018 patch release, which addresses critical bugs including trackpad function in OSX, and display of multiple 3D structures.
+ The full list bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.3b1">2.10.3b1
+ Release Notes</a>. In addition, Jalview 2.10.3 provides:
</p>
<ul>
- <li>Drag and drop reinstated for the Jalview desktop on
- Windows, Linux and older OSX systems.</li>
- <li>Problems loading local PDB files have been fixed</li>
- <li>Conservation shading can be disabled for PID and consensus
- based colour scheme</li>
+ <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><em>Major highlights of the 2.10.0 Release</em></p>
+ <p>
+ <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><br />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>Aligned locus view</strong><br />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>
- <li><strong>Sequence variant data</strong><br />Jalview
- propagates variant annotation on genomic regions onto
- transcripts and protein products, complete with associated
- metadata such as clinical significance.</li>
- </ul></li>
- <li><strong>Ensembl and ENA 'show cross-references'
- support</strong><br />The Calculations menu's <strong>'Show
- cross-references'</strong> now offers Ensembl as well as EMBLCDS and
- Uniprot when CDS/Protein mapping data is available for download or
- display. This allows variant annotation to be added directly to an
- alignment of UniProt sequences.</li>
- <li><strong>Working with structures</strong>
- <ul>
- <li><strong>More accurate structure mappings</strong><br />
- 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><br />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>
- <li><strong>Chimera users will need to upgrade to
- 1.11.1</strong><br />If you use Chimera to view structures
- downloaded by Jalview 2.10, you will need to make sure you are
- running the latest version of <a href="features/chimera.html">Chimera</a>.</li>
- </ul></li>
- <li><strong>UniProt Free Text Search</strong><br />The new
- search dialog for UniProt allows you to browse and retrieve
- sequences with free-text search, or structured queries.</li>
- <li><strong>Reference sequence alignment view</strong><br />
- 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><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>
-
+
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</html>
git://source.jalview.org / jalview.git / blobdiff