What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=cab871c874fb5d1f064fdee0a2f225120c0d1636;hb=refs%2Fheads%2Fbug%2FJAL-2272cmdClickGroupEdit;hp=9eaf83e4352208e8889381ece559ac222f88481d;hpb=e2b0b250d21b61c876bdb2303c34d66922336a86;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 9eaf83e..cab871c 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,130 +1,84 @@ + * 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 2.8 includes a number of enhancements and new features that - have been in development since July 2010. It is also the first Jalview - release to incorporate RNA visualization features developed by Lauren - Lui and Jan Engelhart during their Google Summer of Code projects - (http://code.google.com/soc/). As usual you can find the highlights - below, but to see the comprehensive list take a look at the look at - the Jalview 2.8 Release Notes. -

- Highlights in Jalview Version 2.8 -

Improved JABAWS - client and new JABAWS 2.0 Services - -
- AACon alignment - conservation
- Protein - disorder - DisEMBL, RONN, GlobPlot and IUPred
- Clustal Omega for creating huge protein alignments
RNA -
- Import sequence and alignment associated WUSS or VIENNA - dot-bracket notation from files and the RFAM - database -
- Interactive editing of RNA secondary structure annotation
- Colour scheme for purine/pyrimidine and to highlight RNA - helices
- RNA canonical base pair consensus - score and sequence logo -
- Embedded VARNA RNA - secondary structure viewer in the Desktop -
Parse and display T-COFFEE - alignment quality scores (thanks to Paolo di Tomasso of the Notredame - Group) -
Per - sequence alignment annotation shading
Enhanced PCA viewer: more - export options, and switch between different PCA modes and residue - score models -
New Jalview Desktop database - fetcher GUI -
Support for DAS 1.6 and DAS 2.0 sources (thanks to the new - JDAS Distributed Annotation client library (see - http://code.google.com/p/jdas))
Export sequence database annotation as an HTML report
Normalised Sequence - Logo Display

- Issues resolved in the Jalview Desktop -

PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch - REST service
Stop windows being moved outside desktop on OSX
Jnet job queues forever if a very short sequence is submitted - for prediction
Structure view highlighting doesn't work on windows 7
Jalview desktop fails to launch with exception when using - proxy
DAS Sequence retrieval with range qualification results in - sequence xref which includes range qualification
Cannot close news reader when JABAWS server warning dialog is - shown
Edited sequence not submitted to web service
Jalview 2.7 InstallAnywhere installer doesn't unpack and run - on OSX Mountain Lion -
- If you use webstart then you may need to go into the - Security panel (a.k.a the gatekeeper) in your System - Settings, and select the 'allow any code to run' option. -
-

- Issues specific to the JalviewLite Applet -

Sequence features are momentarily displayed before they are - hidden using hidefeaturegroups applet parameter
loading features via javascript API automatically enables - feature display
scrollToColumnIn javascript API method doesn't work

- Issues affecting both applet and application -

Redundancy removal fails for rna alignment
PCA window shows grey box when first opened on OSX
Letters coloured pink in sequence logo when alignment - coloured with clustalx

+ 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.