</head>
<body>
<p>
- <strong>What's new ?</strong>
+ <strong>What's new in Jalview 2.10.0b1 ?</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 2.10.0b1 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>
- <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
+ <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>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
+ <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>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 <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
+ <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>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>
- 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>
+ 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 alignment view.</strong>.
+ <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><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>
</ul>
</body>
git://source.jalview.org / jalview.git / blobdiff