X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwhatsNew.html;h=448430d6afa3682fefa553af124b0750b0df2a49;hb=refs%2Fheads%2Fspikes%2Fjpred;hp=651292e0b5fa6c4ba15bda5a770cab93160a03b1;hpb=bb105fcca41253815982584f4c8f6fae1f8e10a3;p=jalview.git
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+
What's new ?
-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.
+
-Jalview Version 2.2
-Multiple views with different styles, colours, hidden regions for
-one alignment
-Easily add, amend and delete sequence features
-"Reload" alignment from File or URL to revert to
-original
-"Save" to current filename or "Save As" to
-new filename
-New "New Window" button on the
-"Output To Textbox" opens output window for quick 'sequence
-editing'.
-Set different text colour for dark or light background
-Right align sequence ids
-Set colour of lower case residues in a user defined colour scheme
-
-Menu Rearrangements: New Format for alignment
-layout and Select for region selection.
-
-Menu item accelerator keys added
-Control-V pastes sequences to active window, Control-Shift-V
-pastes to a new window.
-Raise/Minimise alignment and all associated windows from desktop
-window's window menu
-Select and colour whole branches of a tree
-'New Window' button on the 'Output to Text box' alignment output
-option to open a new alignment window after editing.
-Issues Resolved
-
-Optimisations for large alignments: faster multithreaded
-calculations and Undo/Redo system.
-Remove empty columns - if empty columns exist at the end of the
-alignment bug fixed.
-DAS feature fetching slowed down, doesn't overload DAS servers
-DAS feature fetching can be cancelled
-Correct display of > and < symbols for feature descriptions
-without explicit <html> tags.
-Zoom working in PCA viewer
-Sequence Descriptions retained after running a web service
-
-See the Release History page for
-details of all new features and resolved issues.