<html>
-<head><title>What's new ?</title></head>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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+ * This file is part of Jalview.
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+ * Jalview is free software: you can redistribute it and/or
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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>What's new ?</title>
+</head>
<body>
-<p><strong>What's new ?</strong> </p>
-<p>If you are reading this then you will already have seen some of the recent changes
- made to Jalview.<br>
- Jalview takes advantage of some of the more recent user interface developments
- in the Java programming language. For instance Jalview is now a multi windowed
- application, this keeps all your Jalview windows neatly together in one main
- application window. </p>
-<p>If you were familiar with the original Jalview, here is a list of important
- features you should know about the current development:</p>
-<ul>
- <li>Editing sequences is no longer the default when mouse clicking the alignment.
- Instead, mouse clicking on the alignment creates a "selection region"
- which may be full sequences or groups of residues.</li>
- <li>To insert or edit the gaps in one sequence in alignment, the
- "Shift" key must be held down when dragging the mouse.</li>
- <li>To insert or edit gaps for a group of sequences, the
- "Alt" key (or in X windows the "Control"
- key) must be held down.</li>
- <li>Selecting colour schemes in the colour menu either sets just the
- "background" colourscheme for the alignment, or - when
- the tickbox "Apply colour to all groups" is ticked,
- applies the scheme to the background and all groups defined on the alignment.</li>
- <li>Use the right mouse button (apple and click on the Mac) whilst
- the pointer is within the selection area to access the "define" region menu to
- define a new region, give it a name, and change its colourscheme and display
- properties.</li>
- <li>Conservation is automatically updated whenever the alignment is edited</li>
- <li>There is no "quick draw" option</li>
- <li>Edits can be undone, and redone!</li>
-</ul>
+ <p>
+ <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>
+ <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>
</html>
git://source.jalview.org / jalview.git / blobdiff