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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 2.7 release features new web services, and important
- improvements to the way in which Jalview handles alignments and
- associated PDB structures, as well as numerous minor improvements and
- bug fixes. Version 2.7 of the JalviewLite applet also features a
- significantly enhanced Javascript API enabling it to be more easily
- integrated with javascript based web applications.
For full
- details see the Jalview 2.7
- release history.
-
-
- Highlights in Jalview Desktop Version 2.7
-
-
+
+ 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 also allows:
+
+ - Sequence variant data. Jalview
+ propagates variant annotation imported via Ensembl onto
+ 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.
+
+ - 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
+ 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 based alignment
+ visualisation.. 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.
+
+
-
- Issues Resolved (a select list - see the release history for full details)
-
-
-
- Issues in the Jalview Desktop
-
- - Problems viewing associated structures for sequences
- retrieved from UNIPROT
- - Problems viewing Jalview projects from older versions in
- version 2.6
- - Preservation of hidden annotation rows and tree bootstrap
- values in projects
- - Newly added JABAWS servers not always visible in web services
- menu
-
- Issues specific to the JalviewLite Applet
-
- - Layout problems when lots of annotation rows are displayed
- - <= shown as = in annotation row tooltip
- - export features raises exception when no features exist
- - relative URLs not handled properly when used in parameters
- and annotation files
-
- Issues affecting both applet and application
-
- - sequence numbering not preserved in MSF alignment output
- - sequence associated secondary structure not correctly parsed
- in interleaved stockholm
- - sequences containing lowercase letters are not properly
- associated with their pdb files
- - Jalview PDB file reader does not extract sequence from deoxy
- nucleotide chains correctly
- - Sequence length given in alignment properties window is off
- by 1
-