From dbd3bf62a0b201d5b0e410b314de99e204bf6c7d Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 23 Nov 2016 15:36:31 +0000 Subject: [PATCH] =?utf8?q?JAL-2325=20updated=20what=E2=80=99s=20new=20for=20?= =?utf8?q?2.10.1?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- help/html/whatsNew.html | 61 +++-------------------------------------------- 1 file changed, 3 insertions(+), 58 deletions(-) diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 448430d..352941a 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,69 +24,14 @@

- What's new in Jalview 2.10.0b1 ? + What's new in Jalview 2.10.1 ?

- 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 + Jalview 2.10.1 was released on 24th November 2016. Full details are in the Jalview 2.10.1 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.

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