X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=545d55b9a780c803a92270b8e96bcbd50176585e;hb=4497a70ab5bf22b6b6a16c723949625fcca4845b;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 ?
+
+
+ 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
+
+ - 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.
+
+ - 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
+
- 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.
+ 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.
+
+
+
+