What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=736e786392803ba2652d9dd8f443a0b37793bda4;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=9eaf83e4352208e8889381ece559ac222f88481d;hpb=e2b0b250d21b61c876bdb2303c34d66922336a86;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 9eaf83e..736e786 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,130 +1,87 @@ + * 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 ? +

+ Jalview 2.9 has been in development since December 2014. In addition + to a multitude of bug fixes and minor improvements (both small, and + rather big!), it also brings major new capabilities for codon-level + analysis of protein alignments and the retrieval and manipulation of + structural data.

For the full list of changes, see the + Jalview 2.9 Release Notes. +

+ Highlights in Jalview 2.9 +

Visualisation, editing and analysis of + cDNA and Protein alignments
A new Split View window allows linked + protein and nucleotide sequence alignments to be viewed, edited, + and analysed as one.
cDNA alignments can also be + reconstructed from protein alignments calculated by Jalview's web + services, and update in response to edits in the amino acid view.
To + start experimenting with cDNA/Protein analysis, jut drop a file + containing cDNA sequences which code for proteins in an existing + alignment, and Jalview will do the rest.
Enhanced Integration of UCSF Chimera
Jalview + 2.9 provides full support for the use of Chimera to view 3D + structures linked to alignment views in the Jalview Desktop. We've + also included support for saving Chimera sessions in Jalview + project files.
Jalview and Chimera communicate using local + web server connections, which may cause firewall alerts on some + systems, but has the advantage of allowing bidirectional + communication. Communication between Jalview and Chimera is now + much more responsive, and selected regions in Chimera are now + shown as highlighted regions in the Jalview desktop.
Interactive querying of the PDBe
Jalview + users can now browse and retrieve 3D structure data from the PDB + via the PDBe + Search API (Gutmanas + et al 2014). Developed in collaboration with the PDBe group at + EMBL-EBI, the interface allows both structured and free-text + queries to be performed, and allows automatic selection of the + most relevant structures for an alignment acording to a variety of + criteria.
Improved support for RNA visualisation
Jalview + 2.9 integrates the latest version of the VARNA RNA Viewer, and VARNA views + can also now be stored in Jalview projects. We've also dealt with + a number of lingering bugs in the VARNA/Jalview interface, + including the loss of pseudoknots when RNA secondary structure is + shown VARNA.
Protein Secondary Structure predictions + with JPred4
Jalview includes a number of new features for + working with secondary structure predictions from the JPred4 + server. These include new popup menu actions to automatically hide insertions and highlight + mutations in an alignment with respect to a Reference + Sequence. Jalview 2.9's new scrollable + SVG HTML export was also developed specifically for the JPred4 + server.