</head>
<body>
<p>
- <strong>What's new ?</strong>
+ <strong>What's new in Jalview 2.10.1 ?</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.
+ Jalview 2.10.1 was released on 24th November 2016. Full details are in the <a
+ href="releases.html#Jalview.2.10.1">Jalview 2.10.1 Release
+ Notes</a>, but the highlights are below.
</p>
- <p>
- <strong>Highlights in Jalview 2.10</strong>
<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></li>
+ <li><strong>New custom link mechanism for opening URLs for database
+ cross references.</strong><br/> If you have already customised the URL link menu
+ in your Jalview preferences, then you'll already have seen the <a
+ href="webServices/urllinks.html">Update your links warning
+ dialog.</a>
+ </li>
</ul>
</body>
git://source.jalview.org / jalview.git / blobdiff