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<head>
<title>What's new ?</title>
</head>
<body>
- <p>
- <strong>What's new ?</strong><br /> Jalview 2.8.1 includes a range of new features developed in the last 12 months. <br /> As usual you can find the
- highlights below, and the comprehensive list is given in the <a
- href="releases.html#Jalview2.8.1">Jalview 2.8.1 Release Notes</a>.
- </p>
- <strong>Internationalisation</strong>
- <p>
- In August 2013, David Róldan-Martinez took on the task of
- internationalising Jalview's user interface. He also recruited Sara
- Hernández Díaz and Laura Ferrandis Martinez who created Jalview's
- first spanish user interface translation.<br /> If you notice any
- problems, or would like to help translate Jalview's user interface
- into other languages, head over to <a href="http://issues.jalview.org">issues.jalview.org</a>
- and put in a feature request describing the translations you can
- provide to the <a
- href="http://issues.jalview.org/browse/JAL/component/10682">i18n
- component</a>.<br/>
- David has also put together some documentation about getting started with i18n translations
- </p>
- <strong>Enhancements and new features</strong>
- <ul>
- <li>
- <li>Extended the <a href="features/featuresettings.html">feature settings dialog</a> to allow columns to be selected containing particular sequence features.</li>
- </ul>
- <strong>Bug fixes</strong>
- <ul>
- </ul>
+ <p>
+ <strong>What's new in Jalview 2.10.0b1 ?</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.
+ </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>
+ </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>
+
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff