X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=c5859eacb61600f8cbd52cec6104b7bf071affd5;hb=09b25d3dc80f74c0fae97e27fd394417917f3906;hp=448430d6afa3682fefa553af124b0750b0df2a49;hpb=448a82c6838c231172078210cfb1bdad138d4604;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 448430d..c5859ea 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,69 +24,12 @@

- What's new in Jalview 2.10.0b1 ? + What's new in Jalview 2.10.2 ?

- 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

+ Full details about Jalview 2.10.2 are in the + Release Notes, but the highlights are below.

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.