X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=d1d141d30b133f0a400e7fb369ebe9cce029c4d5;hb=53efd00e5fe4b886ede8ec0a6eaa36bc7c8a781e;hp=19be76f59844b47234a5a9550d2f6275656530d3;hpb=ec00ff63b7f8e3259fbbb2895f4c46318bef40c0;p=jalview.git
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- What's new ?
+ What's new in Jalview 2.10.1 ?
- 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.
+ Jalview 2.10.1 was released on 29th November 2016. Full details are
+ in the Jalview 2.10.1
+ Release Notes, but the highlights are below. This is also the
+ first release to include contributions from Kira Mourão, who
+ joined Jalview's core development team in October 2016.
-
- 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.
+ - More memory efficient
We've slimmed
+ down the consensus analysis data structures used by Jalview so
+ even wider alignments can be worked with.
+ - Select highlighted region
Press 'B'
+ or use the new menu option in the alignment window's Select menu
+ to mark columns containing highlighted regions generated from
+ structure selections, mouse-overs, or resulting from a Find
+ operation.
+ - New custom link mechanism for opening URLs
+ for database cross references.
If you have customised URL
+ links in your Jalview preferences, then you may already have seen
+ the warning dialog (see below).
+ - New command line export option for BioJS
+ MSAviewer
A number of small bugs with the HTML export
+ functions from the Jalview desktop were also fixed.
+ - Small but significant changes to the
+ physicochemical properties and consensus calculations
Threonine
+ is no longer considered a non-hydrophobic residue in the protein
+ conservation calculation, and minor bugs addressed in PID and
+ consensus colouring.
+ - Correct display of disulphide bond
+ features
In linked structure views, Jalview would
+ highlight all residues between in addition to the two linked
+ cysteines. The 'select columns by feature' function in the feature
+ settings would also select all intermediate columns.
+
+ Warning dialog about updating
+ your configured URL links
In the desktop prior to Jalview
+ 2.10.1, the only way to configure custom links for a particular
+ database cross-reference for a sequence was to give it a name that exactly
+ matched the database source, and a regular expression for filtering
+ out any spurious matches generated when the custom linked was tested
+ against the Sequence's ID string. Since the introduction of the
+ $DB_ACCESSION$ token, however, $SEQUENCE_ID$ will not be used for
+ database cross-reference accession strings, and if you have custom
+ links configured, Jalview will raise a warning message so let you
+ know that you may need to update your links to use $DB_ACCESSION$.
+