What's new ?
++ What's new ? +
+
+ Jalview 2.8.2 is the first release produced by our new core
+ development team.
It incorporates many minor improvements and
+ bug-fixes, and new features for working with 3D structure data,
+ shading alignments by secondary structure and generation of alignment
+ figures as Scalable Vector Graphics.
The majority of
+ improvements in this version of Jalview concern the desktop
+ application. As ever, the highlights are detailed below,
+ and the full list is given in the Jalview 2.8.2 Release Notes.
+
+ Annotation visualisation
The alignment window
+ includes a new Annotations menu which provides controls for
+ the layout and display of sequence, group and alignment associated
+ annotation rows. It also now includes the Autocalculated
+ Annotation submenu (formerly located in the View menu), which
+ includes settings for the calculation and display of sequence
+ consensus, logos, and amino acid conservation for the alignment and
+ subgroups.
+
+ Sequence associated annotation
New controls
+ have also been added to the Sequence ID popup menu for the propagation
+ and display of sequence associated annotation such as secondary
+ structure assignments and disorder predictions. Annotation associated
+ with one or a group of sequence already shown on the alignment may be
+ shown or hidden, and any available annotation from 3D structure or
+ calculations performed in other Jalview windows can be copied to the
+ alignment
+ via the Add Reference Annotation option.
+ The Colour by annotation function has also been
+ improved, allowing secondary structure annotation to be used to shade
+ sequences and alignment columns. Protein sequences can be coloured
+ according to the presence of a helix or sheet at each position, and
+ RNA sequences can be shaded according to each structure's stem/helix
+ pattern - which enables different RNA folding topologies to be quickly
+ identified.
+
+ 3D Structural data analysis and display
+ Jalview now employs Jmol's PDB data API to retrieve secondary
+ structure assignments made by the DSSP algorithm. It can also employ
+ web services to obtain secondary structure assignments from RNA
+ structures. These assignments are shown as sequence associated
+ annotation for sequences which have cross-references to the PDB, or
+ have had PDB files associated with them via the Structures
+ submenu of the sequence ID popup menu. The extraction and display of
+ secondary structure and B-factor column annotation is controlled via
+ a new Structure tab in the Jalview Desktop's
+ Preferences dialog box.
+
+ Interoperation with UCSF Chimera
The desktop
+ application can now be configured to employ UCSF Chimera for the
+ display of 3D structure data. UCSF Chimera is a python-based
+ high-performance molecular graphics and animation system developed by
+ the Resource for Biocomputing, Visualisation, and Informatics at the
+ University of California.
Jalview employs the 'StructureViz'
+ communication mechanism developed for Cytoscape by Morris et al.
+ (http://www.ncbi.nlm.nih.gov/pubmed/17623706) in 2007. This mechanism
+ allows Jalview to send commands to Chimera, enabling structures to be
+ superimposed and shaded according to associated multiple aligmment
+ views.
Support for Chimera in Jalview 2.8.2 is experimental, and we
+ would appreciate feedback ! Please send your comments to
+ jalview-discuss@jalview.org, and keep up to date with this feature's
+ development via http://issues.jalview.org/browse/JAL-1333.
+
+ Export of alignment figures as Scalable Vector
+ Graphics
Scalable Vector Graphics (SVG) files are now widely
+ supported by web browsers and graphics design programs, and allow
+ high-quality graphics for interactive exploration and publication.
+ Jalview now supports the generation of SVGs interactively (via the
+ Export) menu, and from the command line for server-side figure
+ generation.
+
Jalview Version 2.2
-Multiple views with different styles, colours, hidden regions for one alignment -
-Easily add, amend and delete sequence features -
-"Reload" alignment from File or URL to revert to original -
-"Save" to current filename or "Save As" to new filename -
-Set different text colour for dark or light background -
-Right align sequence ids -
-Set colour of lower case residues in a user defined colour scheme -
-Menu Rearrangements: New Format for alignment layout and Select for region selection. -
-Menu item accelerator keys added -
-Control-V pastes sequences to active window, Control-Shift-V pastes to a new window. -
-Raise/Minimise alignment and all associated windows from desktop window's window menu -
-Select and colour whole branches of a tree
-'New Window' button on the 'Output to Text box' alignment output -option to open a new alignment window after editing.
-Issues Resolved
- --Optimisations for large alignments: faster multithreaded calculations and Undo/Redo system. -
-Remove empty columns - if empty columns exist at the end of the -alignment bug fixed. -
-DAS feature fetching slowed down, doesn't overload DAS servers -
-DAS feature fetching can be cancelled -
-Correct display of > and < symbols for feature descriptions without explicit <html> tags. -
-Zoom working in PCA viewer -
-Sequence Descriptions retained after running a web service -
--
See the Release History page for details of all - new features and resolved issues.