From e5ff0544866ec954e311b7401f5c3989c0016a5e Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 5 Oct 2016 15:53:01 +0100 Subject: [PATCH] JAL-2189 release notes/whats new --- help/html/releases.html | 14 +++++++++----- help/html/whatsNew.html | 11 +++++------ 2 files changed, 14 insertions(+), 11 deletions(-) diff --git a/help/html/releases.html b/help/html/releases.html index 3a8c9f9..6eb42bc 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -90,11 +90,15 @@ Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).

- + Chimera 1.11.1 minimum requirement for viewing structures with Jalview 2.10

- + Retrieve genome, transcript CCDS and gene ids via the Ensembl and Ensembl Genomes REST API +

+ Protein sequence variant annotation computed for 'sequence_variant' annotation on CDS regions (Ensembl)

ENA CDS 'show cross references' for Uniprot sequences

@@ -113,7 +117,7 @@

reinstate CTRL-click for opening pop-up menu on OSX
Export features in Jalview format (again) includes graduated colourschemes
More responsive when working with big alignments and lots of hidden columns
More responsive when working with big alignments and lots of hidden columns
Hidden column markers not always rendered at right of alignment window
Tidied up links in help file table of contents
Feature based tree calculation not shown for DNA alignments
Quality and Conservation are now shown on load even when Consensus calculation is disabled
- +
@@ -186,7 +190,7 @@
Export features should only export the currently displayed features for the current selection or view
Enable 'Get Cross-References' in menu after fetching cross-references
Mouseover of a copy of a sequence is not followed in the structure viewer
Titles for individual alignments in splitframe not restored from project
Titles for individual alignments in splitframe not restored from project
missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default

- What's new ? + What's new in Jalview 2.10 ?

Jalview 2.10 is the next major release in the Jalview 2 series. Full details are in the Jalview 2.10 Release Notes, but the highlights are below.

- Highlights in Jalview 2.10

Ensembl sequence fetcher. Annotated Genes, transcripts and proteinsÂ can be retrieved via Jalview's new , 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.

mmCIF

UniProt Free Text Search. The new search dialog for UniProt allows you to browse and retrieve sequences @@ -73,9 +71,10 @@ sequence. The reference sequence for alignment views can also be saved and restored from Jalview projects.
Ensembl and ENA 'show cross-references' - support.The Calculations menu's 'Show cross-references' will now + support.The Calculations menu's 'Show cross-references' will now offer Ensembl as well as EMBLCDS and Uniprot when CDS/Protein mapping data is available for download or display.

-- 1.7.10.2