From: Jim Procter Date: Tue, 8 Sep 2015 17:00:22 +0000 (+0100) Subject: JAL-1645 first stab at R2.9 “What’s new” X-Git-Tag: Release_2_10_0~457^2~7 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9a881df532ecf49063d4f032144533b9a1a89319;hp=8392c56e80d73084bd8eac9276979bdf28f462a2;p=jalview.git JAL-1645 first stab at R2.9 “What’s new” --- diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 3ee9b32..d124cc8 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -23,86 +23,65 @@ 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. -

+

+ 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 manipulation of structural + data.
For the full list of changes, see the Jalview 2.9 Release Notes. +

+

+ Highlights in Jalview 2.9 + +