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+
What's new ?
-What's new ?
-Jalview Version 2.4
-
- VAMSAS Interoperation Client
- DAS Sequence Fetching
- PFAM full alignment retrieval
- DNA/Protein Product traversal (Experimental)
- .. (more to come)
-
-Issues Resolved
-
+
+ What's new in Jalview 2.10 ?
+
+
+ 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.
+
+
+ - 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:
+
+ - 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.
+ - Sequence variant data
Jalview
+ propagates variant annotation on genomic regions onto
+ transcripts and protein products, complete with associated
+ metadata such as clinical significance.
+
+ - Ensembl and ENA 'show cross-references'
+ support
The Calculations menu's 'Show
+ cross-references' 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.
+ - 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.
+ - 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.
+
+ - UniProt Free Text Search
The new
+ search dialog for UniProt allows you to browse and retrieve
+ sequences with free-text search, or 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.
+
-<--Jalview Version 2.3
-
- Jmol 11.0.2 integration
- PDB views stored in Jalview XML files
- Slide sequences
- Edit sequence in place
- EMBL CDS features
- DAS Feature mapping
- Feature ordering
- Alignment Properties
- Annotation Scores
- Sort by scores
- Feature/annotation editing in applet
-
-Issues Resolved
-
- Headless state operation in 2.2.1
- Incorrect and unstable DNA pairwise alignment
- Cut and paste of sequences with annotation
- Feature group display state in XML
- Feature ordering in XML
- 2.2.1 applet had no feature transparency
- Number pad keys can be used in cursor mode
- Structure Viewer mirror image resolved
-
-->
-
-See the Release History page for
-details of all new features and resolved issues.