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<p>
- <strong>What's new in Jalview 2.10.0b1 ?</strong>
+ <strong>What's new in Jalview 2.10.4 ?</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 May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes:
</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>Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns</li>
+ <li>Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services</li>
+ <li>Critical patches for running Jalview on OSX with Java 10</li>
+ <li>Easier adjustment of the Alignment ID panel and Annotation panel</li>
+ <li>Improved support for mapping between 3D Structures and Uniprot Protein Sequences</li>
+ <li>Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs</li>
+ <li>New buttons on the Structure Chooser for adding structures
+ to an existing view, and disabling automatic superposition
+ according to linked alignments</li>
+ <li>Annotation transfer between Chimera and Jalview <em>(formerly only
+ available in 'Experimental' mode)</em></li>
</ul>
- <p><em>Major highlights of the 2.10.0 Release</em></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>
- </ul>
-
+ <p>
+ The full list of bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.4">2.10.4
+ Release Notes</a>.
+ </p>
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