</head>
<body>
<p>
- <strong>What's new ?</strong>
+ <strong>What's new in Jalview 2.10 ?</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.
</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 also allows:
+ <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>Sequence variant data.</strong> Jalview
- propagates variant annotation imported via Ensembl onto
- protein products, complete with associated metadata such as
- clinical significance.</li>
- <li><strong>Aligned locus view.</strong> Transcripts
+ <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.</li>
+ 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>Working with structures.</strong>
+ <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>
+ <li><strong>More accurate structure mappings</strong><br />
Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI)
- to match structures to UniProt sequences, 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 mmCIF.
- mmCIF files allow Jalview to handle very large structures,
- such as the HIV virus capsid assembly.</li>
+ 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>. 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 based alignment
- visualisation.</strong>. 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></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>
git://source.jalview.org / jalview.git / blobdiff