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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
What's new ?
-
- What's new ?
-
-
- The Jalview 2.8 release features (tbc)
-
For full
- details see the Jalview 2.7.1
- release history.
-
-
- Highlights in Jalview Desktop Version 2.7.1
-
-
-
- - New Purine/Pyrimidine colour scheme
- - Colouring of RNA secondary structure by helices. See Nucleic Acid Support
- - Embedded VARNA RNA secondary structure viewer.
-
+
+ What's new ?
+
+
+ Jalview 2.10 is the next major release in the Jalview 2 series. Full
+ details are in the Jalview
+ 2.10 Release Notes, but the highlights are below.
+
+
+ Highlights in Jalview 2.10
+
+ - Ensembl sequence fetcher. Annotated Genes,
+ transcripts and proteins can be retrieved via Jalview's new Ensembl REST
+ client. Support for import of Ensembl data allows:
+
+ - Sequence variant data. Jalview
+ propagates variant annotation on genomic regions onto transcripts and
+ protein products, complete with associated metadata such as
+ clinical significance.
+ - Aligned locus view. 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.
+
+ - Working with structures.
+
+ - More accurate structure mappings.
+ 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.
+ - Import structures as mmCIF. Jalview
+
- Chimera users will need to upgrade to
+ 1.11.1.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 Chimera.
+ now downloads data from the EMBL-EBI's PDBe site as mmCIF.
+ This allows very large structures to be imported, such as the HIV virus capsid assembly.
+
+ UniProt Free Text Search. The new search
+ dialog for UniProt allows you to browse and retrieve sequences
+ from UniProt with free-text search and more structured queries
+ Reference sequence alignment view..
+ 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.
+ Ensembl and ENA 'show cross-references'
+ support.The Calculations menu's 'Show cross-references' will now
+ offer Ensembl as well as EMBLCDS and Uniprot when CDS/Protein
+ mapping data is available for download or display.
+
-
- Issues Resolved (a select list - see the release history for full details)
-
-
-
- Issues in the Jalview Desktop
-
- Issues specific to the JalviewLite Applet
-
- Issues affecting both applet and application
-