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- What's new ?
+ What's new in Jalview 2.10.5 ?
-
- Jalview 2.9.0b1 is a bug fix release for Jalview 2.9, which has been in development since December 2014. In addition
- to a multitude of bug fixes and minor improvements (both small, and
- rather big!), it also brings major new capabilities for codon-level
- analysis of protein alignments and the retrieval and manipulation of
- structural data.
For the patches since version 2.9 was release, see the
- Jalview 2.9.0b1 Release Notes.
-
-
- Highlights in Jalview 2.9
+
Jalview 2.10.5 is a minor release that includes critical
+ patches for users working with Ensembl, and RNA secondary structure
+ annotation.
- - Visualisation, editing and analysis of
- cDNA and Protein alignments
A new Split View window allows linked
- protein and nucleotide sequence alignments to be viewed, edited,
- and analysed as one.
cDNA alignments can also be
- reconstructed from protein alignments calculated by Jalview's web
- services, and update in response to edits in the amino acid view.
To
- start experimenting with cDNA/Protein analysis, jut drop a file
- containing cDNA sequences which code for proteins in an existing
- alignment, and Jalview will do the rest.
- - Enhanced Integration of UCSF Chimera
Jalview
- 2.9 provides full support for the use of Chimera to view 3D
- structures linked to alignment views in the Jalview Desktop. We've
- also included support for saving Chimera sessions in Jalview
- project files.
Jalview and Chimera communicate using local
- web server connections, which may cause firewall alerts on some
- systems, but has the advantage of allowing bidirectional
- communication. Communication between Jalview and Chimera is now
- much more responsive, and selected regions in Chimera are now
- shown as highlighted regions in the Jalview desktop.
- - Interactive querying of the PDBe
Jalview
- users can now browse and retrieve 3D structure data from the PDB
- via the PDBe
- Search API (Gutmanas
- et al 2014). Developed in collaboration with the PDBe group at
- EMBL-EBI, the interface allows both structured and free-text
- queries to be performed, and allows automatic selection of the
- most relevant structures for an alignment acording to a variety of
- criteria.
- - Improved support for RNA visualisation
Jalview
- 2.9 integrates the latest version of the VARNA RNA Viewer, and VARNA views
- can also now be stored in Jalview projects. We've also dealt with
- a number of lingering bugs in the VARNA/Jalview interface,
- including the loss of pseudoknots when RNA secondary structure is
- shown VARNA.
- - Protein Secondary Structure predictions
- with JPred4
Jalview includes a number of new features for
- working with secondary structure predictions from the JPred4
- server. These include new popup menu actions to automatically hide insertions and highlight
- mutations in an alignment with respect to a Reference
- Sequence. Jalview 2.9's new scrollable
- SVG HTML export was also developed specifically for the JPred4
- server.
+ - 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.
+