X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=84dad7de47c505b824d5e65fa1f82948f8131f86;hb=7bb369b2c881f59430db9c6eba292bf93663e240;hp=1743f1c4fb6a7bf3589622812bf26752e8218d32;hpb=739e52dd5387687cce4831eaafa24116dcaddcb9;p=jalview.git
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- What's new ?
+ What's new in Jalview 2.10.1 ?
- 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.
+ 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.
-
- Highlights in Jalview 2.10
- - 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.
-
- - 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.
+
+ - New custom link mechanism for opening URLs for database
+ cross references.
If you have already customised the URL link menu
+ in your Jalview preferences, then you'll already have seen the Update your links warning
+ dialog.
+