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.