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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23 <title>What's new ?</title>
27 <strong>What's new in Jalview 2.10 ?</strong>
30 Jalview 2.10 is the next major release in the Jalview 2 series. Full
31 details are in the <a href="releases.html#Jalview.2.10.0">Jalview
32 2.10 Release Notes</a>, but the highlights are below.
35 <li><strong>Ensembl sequence fetcher.</strong> Annotated Genes,
36 transcripts and proteins can be retrieved via Jalview's new <a
37 href="features/ensemblsequencefetcher.html">Ensembl REST
38 client</a>. Support for import of Ensembl data allows:
40 <li><strong>Sequence variant data.</strong> Jalview
41 propagates variant annotation on genomic regions onto transcripts and
42 protein products, complete with associated metadata such as
43 clinical significance.</li>
44 <li><strong>Aligned locus view.</strong> Transcripts
45 retrieved for a gene identifier via the Ensembl or
46 EnsemblGenomes sequence databases are automatically aligned to
47 their reference genome, and introns hidden from the view.</li>
49 <li><strong>Working with structures.</strong>
51 <li><strong>More accurate structure mappings.</strong>
52 Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI)
53 to <a href="features/siftsmapping.html">match structures
54 to UniProt sequences</a>, even for structures containing
55 multiple copies of a sequence.</li>
56 <li><strong>Import structures as mmCIF</strong>. Jalview
57 now downloads data from the EMBL-EBI's PDBe site as <a href="features/mmcif.html">mmCIF</a>.
58 This allows very large structures to be imported, such as the HIV virus capsid assembly.</li>
59 <li><strong>Chimera users will need to upgrade to
60 1.11.1.</strong>If you use Chimera to view structures downloaded by
61 Jalview 2.10, you will need to make sure you are running the
62 latest version of <a href="features/chimera.html">Chimera</a>.</li>
64 <li><strong>UniProt Free Text Search.</strong> The new search
65 dialog for UniProt allows you to browse and retrieve sequences
66 from UniProt with free-text search and more structured queries</li>
67 <li><strong>Reference sequence alignment view.</strong>.
68 Jalview 2.9 introduced support for reference sequences. In 2.10,
69 when a reference sequence is defined for the alignment, the
70 alignment column ruler is now numbered according to the reference
71 sequence. The reference sequence for alignment views can also be
72 saved and restored from Jalview projects.</li>
73 <li><strong>Ensembl and ENA 'show cross-references'
74 support.</strong>The Calculations menu's <strong>'Show cross-references'</strong> will now
75 offer Ensembl as well as EMBLCDS and Uniprot when CDS/Protein
76 mapping data is available for download or display.</li>