</head>
<body>
<p>
- <strong>What's new in Jalview 2.10 ?</strong>
+ <strong>What's new in Jalview 2.10.2 ?</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.
+ Full details about Jalview 2.10.2 are in the <a
+ href="releases.html#Jalview.2.10.2"> Release Notes</a>, but the
+ highlights are below.
</p>
<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:
+ <li><strong>Update to JABAWS 2.2</strong><br />Jalview's
+ alignment, protein conservation analysis, and protein disorder and
+ RNA secondary structure prediction services are now provided by <a
+ href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS 2.2</a>.
+ Several of the programs provided as services have been updated, so
+ their options and parameters have changed.</li>
+ <li>New preferences for <a href="webServices/urllinks.html">opening
+ web pages for database cross-references</a> via the UK Elixir's
+ EMBL-EBI's MIRIAM database and identifiers.org services.
+ </li>
+ <li><em>Showing and hiding regions</em>
<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>
+ <li><a href="menus/popupMenu.html#hideinserts">Hide
+ insertions</a> in the PopUp menu has changed its behaviour.
+ Prior to 2.10.2, columns were only shown or hidden according
+ to gaps in the sequence under the popup menu. Now, only
+ columns that are gapped in all selected sequences as well as
+ the sequence under the popup menu are hidden, and column
+ visibility outside the selected region is left as is. This
+ makes it easy to filter insertions from the alignment view
+ (just select the region containing insertions to remove)
+ without affecting the rest of the hidden columns.</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>
- <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>
- </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 <strong>'Show cross-references'</strong> will now
- offer Ensembl as well as EMBLCDS and Uniprot when CDS/Protein
- mapping data is available for download or display.</li>
-
</ul>
-
+ <p>
+ <strong><a name="experimental">Experimental Features</a></strong>
+ </p>
+ <p>
+ This release of Jalview includes a new option in the Jalview Desktop
+ that allows you to try out features that are still in development.
+ To access the features described below, please first enable the <strong>Tools→Enable
+ Experimental Features</strong> option, and then restart Jalview.
+ </p>
+ <ul>
+ <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
+ <a href="features/chimera.html#experimental">new entries in
+ the Chimera viewer's Chimera menu</a> allow positional annotation to
+ be exchanged between Chimera and Jalview.</li>
+ </ul>
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</html>
git://source.jalview.org / jalview.git / blobdiff