X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=19be76f59844b47234a5a9550d2f6275656530d3;hb=1f959f4a5bc07769cde4c2577022ad64e55b4a1a;hp=b81031da3a77ef5ba1792f561e8463c9a157d1f3;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
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What's new ?
-
- What's new ?
- Jalview 2.8 includes a number of enhancements and new features that
- have been in development since July 2010. It is also the first Jalview
- release to incorporate RNA visualization features developed by Lauren
- Lui and Jan Engelhart during their Google Summer of Code projects
- (http://code.google.com/soc/). As usual you can find the highlights
- below, but to see the comprehensive list take a look at the look at
- the Jalview 2.8 Release Notes.
-
- Highlights in Jalview Version 2.8
-
- - Improved JABAWS
- client and new JABAWS 2.0 Services
-
-
- - RNA
-
- - Import sequence and alignment associated WUSS or VIENNA
- dot-bracket notation from files and the RFAM
- database
-
- - Interactive editing of RNA secondary structure annotation
- - Colour scheme for purine/pyrimidine and to highlight RNA
- helices
- - RNA canonical base pair consensus
- score and sequence logo
-
- - Embedded VARNA RNA
- secondary structure viewer in the Desktop
-
-
- - Parse and display T-COFFEE
- alignment quality scores (thanks to Paolo di Tomasso of the Notredame
- Group)
-
- - Per
- sequence alignment annotation shading
- - Enhanced PCA viewer: more
- export options, and switch between different PCA modes and residue
- score models
-
- - New Jalview Desktop database
- fetcher GUI
-
- - Support for DAS 1.6 and DAS 2.0 sources (thanks to the new
- JDAS Distributed Annotation client library (see
- http://code.google.com/p/jdas))
- - Export sequence database annotation as an HTML report
- - Normalised Sequence
- Logo Display
-
-
- Issues resolved in the Jalview Desktop
-
-
- - PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch
- REST service
- - Stop windows being moved outside desktop on OSX
- - Jnet job queues forever if a very short sequence is submitted
- for prediction
- - Structure view highlighting doesn't work on windows 7
- - Jalview desktop fails to launch with exception when using
- proxy
- - DAS Sequence retrieval with range qualification results in
- sequence xref which includes range qualification
- - Cannot close news reader when JABAWS server warning dialog is
- shown
- - Edited sequence not submitted to web service
- - Jalview 2.7 InstallAnywhere installer doesn't unpack and run
- on OSX Mountain Lion
-
- - If you use webstart then you may need to go into the
- Security panel (a.k.a the gatekeeper) in your System
- Settings, and select the 'allow any code to run' option.
-
-
-
-
-
- Issues specific to the JalviewLite Applet
-
-
- - Sequence features are momentarily displayed before they are
- hidden using hidefeaturegroups applet parameter
- - loading features via javascript API automatically enables
- feature display
- - scrollToColumnIn javascript API method doesn't work
-
-
- Issues affecting both applet and application
-
-
- - Redundancy removal fails for rna alignment
- - PCA window shows grey box when first opened on OSX
- - Letters coloured pink in sequence logo when alignment
- coloured with clustalx
-
+
+ What's new ?
+
+
+ Jalview 2.9.0b2 is a bug fix release for Jalview 2.9.
+ The release of Jalview 2.9 in September 2015 included
+ 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 released, see the
+ Jalview 2.9.0b2 Release Notes.
+
+
+ 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.
+
+