X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=448430d6afa3682fefa553af124b0750b0df2a49;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=e6ab69520eb599fea0ced93a73e300673f272971;hpb=c43a1ee36b2679fd972599186e4d6e45fda87623;p=jalview.git
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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
What's new ?
-What's new ?
-Jalview 2.5.1 is a bug fix release for the 2.5 version of
-Jalview. See the release
-history for the bugs that this release resolves.
-Highlights in Jalview Version 2.5
-
- Linked viewing of nucleic acid sequences and structures
- Automatic Scrolling option in View menu to display the
- currently highlighted region of an alignment.
- Order an alignment by sequence length, or using the average score or total feature count for each sequence.
- Shading features by score or associated description
- Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).
- New hide/show options including Shift+Control+H to hide everything but the currently selected region.
-
-Jalview Desktop:
-
- Fetch DB References capabilities and UI expanded to support
- retrieval from DAS sequence sources
- Enable or disable non-positional feature and database
- references in sequence ID tooltip from View menu in application.
- Group-associated consensus, sequence logos and conservation
- plots
- Symbol distributions for each column can be exported and
- visualized as sequence logos
- Jalview Java Console
- New webservice for submitting sequences and IDs to Envision2 Workflows
- Improved VAMSAS synchronization and sharing of selections.
-
-JalviewLite:
-
- Middle button resizes annotation row height
- New Parameters - including default tree display settings.
- Non-positional features displayed in ID tooltip
-
-Issues Resolved (a select list)
-
-
- Source field in GFF files parsed as feature source rather
- than description
- Non-positional features are now included in sequence feature
- and gff files (controlled via non-positional feature visibility in
- tooltip).
- URL links generated for all feature links (bugfix)
- Codons containing ambiguous nucleotides translated as 'X' in
- peptide product
- Match case switch in find dialog box works for both sequence
- ID and sequence string and query strings do not have to be in upper
- case to match case-insensitively.
- Jalview Annotation File generation/parsing consistent with
- documentation (e.g. Stockholm annotation can be exported and
- re-imported)
- Find incrementally searches ID string matches as well as
- subsequence matches, and correctly reports total number of both.
-
- Desktop Issues
-
- Better handling of exceptions during sequence retrieval
- PDB files retrieved from URLs are cached properly
- Sequence description lines properly shared via VAMSAS
- Sequence fetcher fetches multiple records for all data
- sources
- Ensured that command line das feature retrieval completes
- before alignment figures are generated.
- Reduced time taken when opening file browser for first time.
- User defined group colours properly recovered from Jalview projects.
-
-
+
+ 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.
+
-
-See the Release History page for
-details of all new features and resolved issues.