What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=fe70fb48d89f1d03410c47b15e2785e9726a6399;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=5d00e193e35918a376d012edd2cd0629fa9d422f;hpb=0bce27989320cd0b44a13151269749614d5cd312;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 5d00e19..fe70fb4 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,7 +1,7 @@ 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 some 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 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 2.8.1 includes new features for group creation, RNA secondary + structure prediction and a host bug fixes. It also includes support + for version 2.1 + of JABA and includes a Spanish translation of its user interface.
+ The highlights are detailed below, and the full list is given in the Jalview 2.8.1 Release Notes. +

The Desktop and web based applet include new keystrokes for + defining and undefining groups, and PAM250 has been added to the range + of score models available for use by the tree and PCA calculations. + The Jalview project file format has also been extended for handling + RNA and protein secondary structure annotation, in anticipation for + new structure based secondary structure support in Jalview 2.8.2.

Internationalisation

Jalview 2.8.1 is the first release to include support for + displaying Jalview's user interface in different languages. In August + 2013, David Roldán-Martinez took on the task of + internationalising Jalview's user interface. He also recruited Sara + Hernández Díaz and Laura Ferrandis Martinez who created + Jalview's first spanish user interface translation.

+ If you notice any problems, or would like to help translate Jalview's + user interface into other languages, head over to issues.jalview.org and put in a + feature request describing the translations you can provide to the i18n + component. David has also documented + the process of creating i18n translations to help you get started. +

RNA Secondary Structure Prediction with JABA 2.1

+ This version of Jalview includes a client to access the new services available in JABA v2.1 , which + provides services for RNA consensus secondary structure prediction and + two new alignment programs (GLProbs and MSAProbs).

+ To see how to perform RNA secondary structure predictions like the one below, take a look at the RNAAliFold + client documentation. +

The RNAalifold client was implemented by Jalview's 2013 + summer student, Dan Barton. +