X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=ed6f5c263624db37d6154d3345604ad82f6b3c89;hb=a4806ceb8d534d99eb00fbf9157ff79c95da0939;hp=1743f1c4fb6a7bf3589622812bf26752e8218d32;hpb=739e52dd5387687cce4831eaafa24116dcaddcb9;p=jalview.git
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- 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 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.
+
- 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 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.
+ - 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.
+