What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=448430d6afa3682fefa553af124b0750b0df2a49;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=cf96d474e209855f2d8c501f9bb9c81286f6b97b;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index cf96d47..448430d 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,103 +1,93 @@ + * 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 ? -

- The Jalview 2.7 release features new web services, and important - improvements to the way in which Jalview handles alignments and - associated PDB structures, as well as numerous minor improvements and - bug fixes. Version 2.7 of the JalviewLite applet also features a - significantly enhanced Javascript API enabling it to be more easily - integrated with javascript based web applications.
For full - details see the Jalview 2.7 - release history. -

- Highlights in Jalview Desktop Version 2.7 -

New structure viewer - options: -
- Colour and superimpose 3D structures of complexes and - multi-domain chains using several different alignments
- Drag and drop to associate PDB files with sequences that - have the same name
- Open and superimpose all associated structures for the - current selection
-
New web services for alignment - analysis
Improved graphical user interface for JABAWSservices. -
Sort associated alignment views option in tree viewer
Default colours for shading alignment - by quantitative annotation. -
Jalview Desktop RSS - reader - following important updates at http://www.jalview.org/feeds/desktop/rss -

+ 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.

- Issues Resolved (a select list - see the release history for full details) - -

- Issues in the Jalview Desktop -

Problems viewing associated structures for sequences - retrieved from UNIPROT
Problems viewing Jalview projects from older versions in - version 2.6
Preservation of hidden annotation rows and tree bootstrap - values in projects
Newly added JABAWS servers not always visible in web services - menu

- Issues specific to the JalviewLite Applet -

Layout problems when lots of annotation rows are displayed
<= shown as = in annotation row tooltip
export features raises exception when no features exist
relative URLs not handled properly when used in parameters - and annotation files

- Issues affecting both applet and application -

sequence numbering not preserved in MSF alignment output
sequence associated secondary structure not correctly parsed - in interleaved stockholm
sequences containing lowercase letters are not properly - associated with their pdb files
Jalview PDB file reader does not extract sequence from deoxy - nucleotide chains correctly
Sequence length given in alignment properties window is off - by 1