X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=cab871c874fb5d1f064fdee0a2f225120c0d1636;hb=999da17dfcc3433b96f3a7e34458749573321e3e;hp=7bc6de4d46b346bf9999fdd9ccee266b31088471;hpb=1162b546d4804d709920737049d796a5a9aa71e1;p=jalview.git
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-
-
What's new ?
-
-What's new ?
-Jalview Version 2.07
-Sequence Fetcher has been added to quickly
- retrieve sequences with known ids from several databases.
-Sequence Features enhanced to allow
- the user to display all features of a Uniprot file on the alignment and subsequently
- colour, hide or show overlapping features.
-Choose to omit /start-end from sequences when
- saving files. This is important for saving files to be used by some programs
- which cannot read the original Jalview sequence output with the appended /start-end.
-PDB structure viewer enhanced. Mapping
- between sequence and structure has been enhanced, colours on the alignment are
- reflected in the structure viewer.
-Jalview Applet can read
- in feature files, PDB files be used as input to HTML form See the website
- to find out the new parameters available for the Applet Version of Jalview.
-
-Issues Resolved
-Group Editing is possible with Control and mouse click. Alt key and mouse press
- does not work as this translates as the middle mouse button, which since 2.04
- is now used to scroll the alignment and change the font size.
-HTML export now writes groups and features which were previously missing.
-
-See the Release History page for details of all
- new features and resolved issues.
-
-
+
+
+
+What's new ?
+
+
+
+ What's new in Jalview 2.10 ?
+
+
+ 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.
+
+
+ - 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.
+
+
+
+