What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=448430d6afa3682fefa553af124b0750b0df2a49;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=3ee9b32a21d92f42abb4207696b2c84c893552dd;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 3ee9b32..448430d 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -23,86 +23,71 @@ 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 in Jalview 2.10.0b1 ? +

+ Jalview 2.10.0b1 is a patch release for 2.10, the next major release + in the Jalview 2 series. Full details are in the Jalview 2.10b1 Release + Notes, but the highlights are below. +

Drag and drop reinstated for the Jalview desktop on + Windows, Linux and older OSX systems.
Problems loading local PDB files have been fixed
Conservation shading can be disabled for PID and consensus + based colour scheme

Major highlights of the 2.10.0 Release

Ensembl sequence fetcher
Annotated + Genes, transcripts and proteins can be retrieved via Jalview's new + Ensembl REST + client. Support for import of Ensembl data allows: +
- Aligned locus view
  Transcripts + retrieved for a gene identifier via the Ensembl or + EnsemblGenomes sequence databases are automatically aligned to + their reference genome, and introns hidden from the view.
- Sequence variant data
  Jalview + propagates variant annotation on genomic regions onto + transcripts and protein products, complete with associated + metadata such as clinical significance.
Ensembl and ENA 'show cross-references' + support
The Calculations menu's 'Show + cross-references' now offers Ensembl as well as EMBLCDS and + Uniprot when CDS/Protein mapping data is available for download or + display. This allows variant annotation to be added directly to an + alignment of UniProt sequences.
Working with structures +
- More accurate structure mappings
  + Jalview now utilises the PDBe's SIFTS database (at EMBL-EBI) + to match structures + to UniProt sequences, even for structures containing + multiple copies of a sequence.
- Import structures as mmCIF
  Jalview + now downloads data from the EMBL-EBI's PDBe site as mmCIF. This allows very large + structures to be imported, such as the HIV virus capsid + assembly.
- Chimera users will need to upgrade to + 1.11.1
  If you use Chimera to view structures + downloaded by Jalview 2.10, you will need to make sure you are + running the latest version of Chimera.
UniProt Free Text Search
The new + search dialog for UniProt allows you to browse and retrieve + sequences with free-text search, or structured queries.
Reference sequence alignment view
+ Jalview 2.9 introduced support for reference sequences. In 2.10, + when a reference sequence is defined for the alignment, the + alignment column ruler is now numbered according to the reference + sequence. The reference sequence for alignment views can also be + saved and restored from Jalview projects.