X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=0abd2a7b9501e9f1fffc3bc4456f39ec4af1d50a;hb=0e684f72690bd6532272a39ab6c188a27559fd09;hp=67d89b79a9513ccc08758c4201b945368f8ab8d4;hpb=b88ac108faaae71ea9681f716232161752b7d789;p=jalview.git
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- What's new ?
+ What's new in Jalview 2.10.4 ?
- 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.
+ This is the May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes:
-
- Highlights in Jalview 2.9
- - 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.
+ - Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns
+ - Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services
+ - Critical patches for running Jalview on OSX with Java 10
+ - Easier adjustment of the Alignment ID panel and Annotation panel
+ - Improved support for mapping between 3D Structures and Uniprot Protein Sequences
+ - Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs
+ - New buttons on the Structure Chooser for adding structures
+ to an existing view, and disabling automatic superposition
+ according to linked alignments
+ - Annotation transfer between Chimera and Jalview (formerly only
+ available in 'Experimental' mode)
-
+
+ The full list of bugs fixed in this release can be found in the 2.10.4
+ Release Notes.
+