X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=0abd2a7b9501e9f1fffc3bc4456f39ec4af1d50a;hb=31117f8593d9c51c6238be3d40771819da96939d;hp=21e6ffa7dff84b9c0342906e448b761c1027c526;hpb=e5ff0544866ec954e311b7401f5c3989c0016a5e;p=jalview.git
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- What's new in Jalview 2.10 ?
+ What's new in Jalview 2.10.4 ?
- 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.
+ This is the May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes:
- - 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:
-
- - Sequence variant data. Jalview
- propagates variant annotation on genomic regions onto transcripts and
- 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, and introns hidden from the view.
-
- - 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
- from UniProt with free-text search and more 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.
- - Ensembl and ENA 'show cross-references'
- 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.
-
+ - 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.
+