X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=736e786392803ba2652d9dd8f443a0b37793bda4;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=b5f5c7876eead6be00bda53d2434f747f09c3d2d;hpb=6fc9aca27f606f6e3a0121597896e1a5dae35c36;p=jalview.git
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-
-What's new ?
-
-What's new ?
-Jalview Version 2.08
- Editing can be locked to the selection area.
- Any edits made within the locked area do not affect the rest of the alignment.
- Keyboard editing - press F2 to toggle cursor mode On / Off. For a full list
- of keyboard controls, look here.
- Create sequence features from searches.
- Previously, the regions of sequences highlighted as the result of
- searches were added as new regions in the alignment. Now, the sequence region
- selected by a search can be used to define named sequences features
- attached to the sequence, rather than the alignment.
-
-Sequence feature display and rendering has also been enhanced, with
- the addition of sequence feature groups (which can be used to show
- or hide a set of feature types en masse) and user defined
- feature colours as well as transparency controls, using the Sequence Feature Settings
- window. The Features file
- has also been extended to accomodate these enhancements.
-Alignment annotation and colouring is also considerably
- enhanced. Precalculated symbolic and quantitative annotations (text labels,
- secondary structure symbols and multiple scalar graphs) can now be
- loaded onto alignments via the Annotation
- File. Additionally, the Annotation
- Colouring dialog box allows an alignment to be coloured based on
- any of the graphed quantities with which it is annotated.
-Rendering speed has been improved by disabling anti-aliasing via
- the Smooth Fonts
- option in the View
- menu (its default set in Preferences). In addition, response
- times when editing alignments can be reduced by turning off the automatic
- calculation of amino acid property Consensus (which has been
- reintroduced to the Calculate menu as Autocalculate Consensus).
-
-Issues Resolved
-
-- Drag & Drop now works on common Linux desktops (at least KDE
-and Gnome)
-- Jalview XML Archive Input/Output is now faster (using an
-internal Jalview schema), and sequence description strings are now
-preserved in the archive.
-- Jalview can now correctly read and write MODELLER style
-PIR description lines for proteins with a PDB reference.
-
-
-See the Release History page for details of all
- new features and resolved issues.
-
-
+
+
+
+What's new ?
+
+
+
+ What's new ?
+
+
+ Jalview 2.9 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 full list of changes, see the
+ Jalview 2.9 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.
+
+
+
+