- 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.
-
+ What's new in Jalview 2.10.5 ? +
+Jalview 2.10.5 is a minor release that includes critical + patches for users working with Ensembl, and RNA secondary structure + annotation.
++ The full list of bugs fixed in this release can be found in the 2.10.5 Release Notes. The majority of improvement in 2.10.5 are due to Jalview users + contacting us via the jalview-discuss email list. Thanks to everyone + who took the time to do this !
+Jalview and Java 10
+This release addresses a critical bug for OSX users who are + running Jalview with Java 10 which can prevent files being saved + correctly through the 'Save As' dialog box. The 'Save As' dialog for + Jalview's Groovy Console remains affected - we hope to address this + in the next major release.