X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=448430d6afa3682fefa553af124b0750b0df2a49;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=7d88e7f5eafbbbd8e2e11aa21b479e5d6c6588d5;hpb=2e2bc3fbb0231c705e5d019df9cb8e0e600ca12e;p=jalview.git
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-
-What's new ?
-
-What's new ?
-Jalview Version 2.08
-Editing can be locked to the
- selection area so that any edits made within the locked area do
- not unexpectedly shift other parts of the alignment.
- Keyboard editing - press F2 to toggle cursor mode On / Off. For a full list
- of keyboard controls, look here.
- Create sequence features from searches.
- Previously, the regions of sequences highlighted as the result of
- searches were added as new regions in the alignment. Now, the sequence region
- selected by a search can be used to define named sequences features
- attached to the sequence, rather than the alignment.
-
-Sequence feature display and rendering has also been enhanced, with
- the addition of sequence feature groups (which can be used to show
- or hide a set of features en masse) and user defined
- feature colours as well as transparency controls, using the Sequence Feature Settings
- window. The Features file
- has also been extended to accomodate these enhancements.
-Alignment annotation and colouring is also considerably
- enhanced. Precalculated symbolic and quantitative annotations (text labels,
- secondary structure symbols and multiple scalar graphs) can now be
- loaded onto alignments via the Annotation
- File. Additionally, the Annotation
- Colouring dialog box allows an alignment to be coloured based on
- any of the graphed quantities with which it is annotated.
-Rendering speed has been improved by disabling anti-aliasing via
- the Smooth Fonts
- option in the View
- menu (its default set in Preferences). In addition, response
- times when editing alignments can be reduced by turning off the automatic
- calculation of amino acid property Consensus (which has been
- reintroduced to the Calculate menu as Autocalculate Consensus).
-
-Issues Resolved
-
-- Drag & Drop now works on common Linux desktops (at least KDE
-and Gnome)
-- Jalview XML Archive Input/Output is now faster (using an
-internal Jalview schema), and sequence description strings are now
-preserved in the archive.
-- Jalview can now correctly read and write MODELLER style
-PIR files.
-
-
-See the Release History page for details of all
- new features and resolved issues.
-
-
+
+
+
+What's new ?
+
+
+
+ What's new in Jalview 2.10.0b1 ?
+
+
+ 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.
+
+
+ - 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.
+
+
+
+