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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
<title>What's new ?</title>
</head>
<body>
- <p>
- <strong>What's new ?</strong>
- </p>
- <p>
- Jalview 2.8.2 is the first release produced by our new core
- development team.<br /> It incorporates many minor improvements and
- bug-fixes, and also includes new features for working with 3D
- structure data, shading alignments by secondary structure and
- generation of alignment figures as Scalable Vector Graphics. <br />As
- ever, the highlights are detailed below, and the full list is given in
- the <a href="releases.html#Jalview2.8.2">Jalview 2.8.2 Release
- Notes</a>.
- </p>
+ <p>
+ <strong>What's new ?</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:
+ <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
+ retrieved for a gene identifier via the Ensembl or
+ EnsemblGenomes sequence databases are automatically aligned to
+ their reference genome.</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 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>
+ </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>
+ </ul>
+
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git://source.jalview.org / jalview.git / blobdiff