X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=ac086c813833e3225cf24116a9aa88386e1d96d6;hb=5dd170e1f8135791b8e5e2670b095bbd6009d3a6;hp=e1b00c4d8cc42b2cac8f7202446613fce070e204;hpb=7ee8954fcde2074b3418a4c58d4e091bc6064315;p=jalview.git
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- What's new ?
+ What's new in Jalview 2.10.5 ?
-
- 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
+
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 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.
-
+ - 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.
+