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- 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.
+ What's new in Jalview 2.10.5 ?
+ Jalview 2.10.5 is a minor release that includes critical
+ patches for users working with Ensembl, and RNA secondary structure
+ annotation.
- - 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.
+ - EPS, PNG and SVG export now includes hidden sequence
+ markers, and representative sequences are marked in bold.
+ - Ensembl Client updated for Ensembl Rest API v7.
The
+ latest Ensembl API is not backwards compatible with earlier
+ versions of Jalview, so if you require Ensembl functionality you
+ will need to install this release.
+
+ - Improved support for VIENNA extended dot-bracket notation
+ for RNA secondary structure
+ - Positional and selected region highlighting in VARNA
+ 'trimmed sequence' view now more reliable
-
+ The majority of improvement in 2.10.5 are due to Jalview users
+ contacting us via the jalview-discuss email list. Thanks to everyone
+ who took the time to do this !
+
+ The full list of bugs fixed in this release can be found in the 2.10.5 Release Notes.
+