</head>
<body>
<p>
- <strong>What's new ?</strong>
+ <strong>What's new in Jalview 2.10.0b1 ?</strong>
</p>
<p>
- Jalview 2.9 has been in development since December 2014. In addition
- to a multitude of bug fixes and minor improvements (both small, and
- rather big!), it also brings major new capabilities for codon-level
- analysis of protein alignments and the retrieval and manipulation of
- structural data.</p><p>For the full list of changes, see the
- <a href="releases.html#Jalview.2.9">Jalview 2.9 Release Notes</a>.
+ 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 2.9</strong>
<ul>
- <li><strong>Visualisation, editing and analysis of
- cDNA and Protein alignments</strong><br />A new <a
- href="features/splitView.html">Split View</a> window allows linked
- protein and nucleotide sequence alignments to be viewed, edited,
- and analysed as one. <br />cDNA alignments can also be
- reconstructed from protein alignments calculated by Jalview's web
- services, and update in response to edits in the amino acid view.<br />To
- start experimenting with cDNA/Protein analysis, jut drop a file
- containing cDNA sequences which code for, and have IDs matching
- proteins in an existing alignment, and Jalview will do the rest.</li>
- <li><strong>Enhanced Integration of UCSF Chimera</strong> <br>Jalview
- 2.9 provides full support for the use of Chimera to view 3D
- structures linked to alignment views in the Jalview Desktop. We've
- also included support for saving Chimera sessions in Jalview
- project files.<br />Jalview and Chimera communicate using local
- web server connections, which may cause firewall alerts on some
- systems, but has the advantage of allowing bidirectional
- communication. Communication between Jalview and Chimera is now
- much more responsive, and selected regions in Chimera are now
- shown as highlighted regions in the Jalview desktop.</li>
- <li><strong>Interactive querying of the PDBe</strong><br />Jalview
- users can now browse and retrieve 3D structure data from the PDB
- via the <a href="http://www.ebi.ac.uk/pdbe/api/doc/search.html">PDBe
- Search API</a> (<a href="http://dx.doi.org/10.1093%2Fnar%2Fgkt1180">Gutmanas
- et al 2014</a>). Developed in collaboration with the PDBe group at
- EMBL-EBI, the interface allows both structured and free-text
- queries to be performed, and allows automatic selection of the
- most relevant structures for an alignment acording to a variety of
- criteria.</li>
- <li><strong>Improved support for RNA visualisation</strong><br />Jalview
- 2.9 integrates the latest version of the <a
- href="http://varna.lri.fr">VARNA RNA Viewer</a>, and VARNA views
- can also now be stored in Jalview projects. We've also dealt with
- a number of lingering bugs in the VARNA/Jalview interface,
- including the loss of pseudoknots when RNA secondary structure is
- shown VARNA.</li>
- <li><strong>Protein Secondary Structure predictions
- with JPred4</strong><br/>Jalview includes a number of new features for working
- with secondary structure predictions from the JPred4 server. These
- include the ability to automatically hide insertions and highlight
- mutations in an alignment with respect to a reference sequence.
- Jalview 2.9's new <a href="io/export.html#htmlexport">scrollable SVG HTML export</a> was also
- developed specifically for the JPred4 server.</li>
+ <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>
git://source.jalview.org / jalview.git / blobdiff