X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=d1d141d30b133f0a400e7fb369ebe9cce029c4d5;hb=47fd498a6fe7d2e3350a9e87c526bf1e59d00be5;hp=448430d6afa3682fefa553af124b0750b0df2a49;hpb=448a82c6838c231172078210cfb1bdad138d4604;p=jalview.git
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- What's new in Jalview 2.10.0b1 ?
+ What's new in Jalview 2.10.1 ?
- Jalview 2.10.0b1 is a patch release for 2.10, the next major release
- in the Jalview 2 series. Full details are in the Jalview 2.10b1 Release
- Notes, but the highlights are below.
+ Jalview 2.10.1 was released on 29th November 2016. Full details are
+ in the Jalview 2.10.1
+ Release Notes, but the highlights are below. This is also the
+ first release to include contributions from Kira Mourão, who
+ joined Jalview's core development team in October 2016.
- - Drag and drop reinstated for the Jalview desktop on
- Windows, Linux and older OSX systems.
- - Problems loading local PDB files have been fixed
- - Conservation shading can be disabled for PID and consensus
- based colour scheme
-
- Major highlights of the 2.10.0 Release
-
- - 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:
-
- - 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.
- - Sequence variant data
Jalview
- propagates variant annotation on genomic regions onto
- transcripts and protein products, complete with associated
- metadata such as clinical significance.
-
- - Ensembl and ENA 'show cross-references'
- support
The Calculations menu's 'Show
- cross-references' now offers Ensembl as well as EMBLCDS and
- Uniprot when CDS/Protein mapping data is available for download or
- display. This allows variant annotation to be added directly to an
- alignment of UniProt sequences.
- - 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 with free-text search, or 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.
+ - More memory efficient
We've slimmed
+ down the consensus analysis data structures used by Jalview so
+ even wider alignments can be worked with.
+ - Select highlighted region
Press 'B'
+ or use the new menu option in the alignment window's Select menu
+ to mark columns containing highlighted regions generated from
+ structure selections, mouse-overs, or resulting from a Find
+ operation.
+ - New custom link mechanism for opening URLs
+ for database cross references.
If you have customised URL
+ links in your Jalview preferences, then you may already have seen
+ the warning dialog (see below).
+ - New command line export option for BioJS
+ MSAviewer
A number of small bugs with the HTML export
+ functions from the Jalview desktop were also fixed.
+ - Small but significant changes to the
+ physicochemical properties and consensus calculations
Threonine
+ is no longer considered a non-hydrophobic residue in the protein
+ conservation calculation, and minor bugs addressed in PID and
+ consensus colouring.
+ - Correct display of disulphide bond
+ features
In linked structure views, Jalview would
+ highlight all residues between in addition to the two linked
+ cysteines. The 'select columns by feature' function in the feature
+ settings would also select all intermediate columns.
+
+ Warning dialog about updating
+ your configured URL links
In the desktop prior to Jalview
+ 2.10.1, the only way to configure custom links for a particular
+ database cross-reference for a sequence was to give it a name that exactly
+ matched the database source, and a regular expression for filtering
+ out any spurious matches generated when the custom linked was tested
+ against the Sequence's ID string. Since the introduction of the
+ $DB_ACCESSION$ token, however, $SEQUENCE_ID$ will not be used for
+ database cross-reference accession strings, and if you have custom
+ links configured, Jalview will raise a warning message so let you
+ know that you may need to update your links to use $DB_ACCESSION$.
+