3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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16 * PURPOSE. See the GNU General Public License for more details.
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20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>What's new ?</title>
27 <strong>What's new in Jalview 2.10.0b1 ?</strong>
30 Jalview 2.10.0b1 is a patch release for 2.10, the next major release
31 in the Jalview 2 series. Full details are in the <a
32 href="releases.html#Jalview.2.10.0b1">Jalview 2.10b1 Release
33 Notes</a>, but the highlights are below.
36 <li>Drag and drop reinstated for the Jalview desktop on
37 Windows, Linux and older OSX systems.</li>
38 <li>Problems loading local PDB files have been fixed</li>
39 <li>Conservation shading can be disabled for PID and consensus
40 based colour scheme</li>
42 <p><em>Major highlights of the 2.10.0 Release</em></p>
44 <li><strong>Ensembl sequence fetcher</strong><br />Annotated
45 Genes, transcripts and proteins can be retrieved via Jalview's new
46 <a href="features/ensemblsequencefetcher.html">Ensembl REST
47 client</a>. Support for import of Ensembl data allows:
49 <li><strong>Aligned locus view</strong><br />Transcripts
50 retrieved for a gene identifier via the Ensembl or
51 EnsemblGenomes sequence databases are automatically aligned to
52 their reference genome, and introns hidden from the view.</li>
53 <li><strong>Sequence variant data</strong><br />Jalview
54 propagates variant annotation on genomic regions onto
55 transcripts and protein products, complete with associated
56 metadata such as clinical significance.</li>
58 <li><strong>Ensembl and ENA 'show cross-references'
59 support</strong><br />The Calculations menu's <strong>'Show
60 cross-references'</strong> now offers Ensembl as well as EMBLCDS and
61 Uniprot when CDS/Protein mapping data is available for download or
62 display. This allows variant annotation to be added directly to an
63 alignment of UniProt sequences.</li>
64 <li><strong>Working with structures</strong>
66 <li><strong>More accurate structure mappings</strong><br />
67 Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI)
68 to <a href="features/siftsmapping.html">match structures
69 to UniProt sequences</a>, even for structures containing
70 multiple copies of a sequence.</li>
71 <li><strong>Import structures as mmCIF</strong><br />Jalview
72 now downloads data from the EMBL-EBI's PDBe site as <a
73 href="features/mmcif.html">mmCIF</a>. This allows very large
74 structures to be imported, such as the HIV virus capsid
76 <li><strong>Chimera users will need to upgrade to
77 1.11.1</strong><br />If you use Chimera to view structures
78 downloaded by Jalview 2.10, you will need to make sure you are
79 running the latest version of <a href="features/chimera.html">Chimera</a>.</li>
81 <li><strong>UniProt Free Text Search</strong><br />The new
82 search dialog for UniProt allows you to browse and retrieve
83 sequences with free-text search, or structured queries.</li>
84 <li><strong>Reference sequence alignment view</strong><br />
85 Jalview 2.9 introduced support for reference sequences. In 2.10,
86 when a reference sequence is defined for the alignment, the
87 alignment column ruler is now numbered according to the reference
88 sequence. The reference sequence for alignment views can also be
89 saved and restored from Jalview projects.</li>