X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=ed6f5c263624db37d6154d3345604ad82f6b3c89;hb=a4806ceb8d534d99eb00fbf9157ff79c95da0939;hp=e1b00c4d8cc42b2cac8f7202446613fce070e204;hpb=7ee8954fcde2074b3418a4c58d4e091bc6064315;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index e1b00c4..ed6f5c2 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,51 +24,57 @@

- What's new ? + What's new in Jalview 2.10.4b1 ?

- 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 +

This is the first patch release for Jalview 2.10.4. It includes + the following new patches:

Ensembl sequence fetcher. Annotated Genes, - transcripts and proteinsÂ can be retrieved via Jalview's new Ensembl REST - client. Support for import of Ensembl data also allows: -
- Sequence variant data. Jalview - propagates variant annotation imported via Ensembl onto - protein products, complete with associated metadata such as - clinical significance.
- Aligned locus view. Transcripts - retrieved for a gene identifier via the Ensembl or - EnsemblGenomes sequence databases are automatically aligned to - their reference genome.
Working with structures. +
HGVS nomenclature used for variant annotation retrieved + from Uniprot
Uniprot import fails for some sequences (Cannot import + features with multiple variant elements)
Clustal files with sequence positions in right-hand column + are now parsed correctly
Wrap view - export to SVG - IDs shown but not alignment + area in exported graphic
F2/Keyboard mode edits work when Overview window has input + focus
Windows specific fixes:
- 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.
UniProt Free Text Search. The new search - dialog for UniProt allows you to browse and retrieve sequences - from UniProt with free-text search and more structured queries
Reference sequence based alignment - visualisation.. 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.
Annotation panel set too high when annotation added to + view
Updated search paths for Chimera default installation
Windows File Shortcuts can be dragged onto the Jalview + Desktop
Drag URL from Chrome, Firefox, IE to Jalview desktop on + Windows doesn't open file:
Dragging the currently open + URL and links from a page viewed in Firefox or Chrome on + Windows is now fully supported.
+ If you are using Edge, only links in the page + can be dragged.
+ With Internet Explorer, only the currently open + URL in the browser can be dropped onto Jalview. +

+ - +

Highlights in the 2.10.4 series include:

Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns
Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services
Critical patches for running Jalview on OSX with Java 10
Easier adjustment of the Alignment ID panel and Annotation panel
Improved support for mapping between 3D Structures and Uniprot Protein Sequences
Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs
New buttons on the Structure Chooser for adding structures + to an existing view, and disabling automatic superposition + according to linked alignments
Annotation transfer between Chimera and Jalview (formerly only + available in 'Experimental' mode)

+ The full list of bugs fixed in this release can be found in the 2.10.4 + Release Notes. +