The RNAalifold client was implemented by Jalview's 2013 + summer student, Dan Barton. +
What's new ?
-Jalview Version 2.08
-Editing can be locked to the - selection area so that any edits made within the locked area do - not unexpectedly shift other parts of the alignment.
-Keyboard editing - press F2 to toggle cursor mode On / Off. For a full list - of keyboard controls, look here.
-Create sequence features from searches. - Previously, the regions of sequences highlighted as the result of - searches were added as new regions in the alignment. Now, the sequence region - selected by a search can be used to define named sequences features - attached to the sequence, rather than the alignment. -
-Sequence feature display and rendering has also been enhanced, with - the addition of sequence feature groups (which can be used to show - or hide a set of features en masse) and user defined - feature colours as well as transparency controls, using the Sequence Feature Settings - window. The Features file - has also been extended to accomodate these enhancements.
-Alignment annotation and colouring is also considerably - enhanced. Precalculated symbolic and quantitative annotations (text labels, - secondary structure symbols and multiple scalar graphs) can now be - loaded onto alignments via the Annotation - File. Additionally, the Annotation - Colouring dialog box allows an alignment to be coloured based on - any of the graphed quantities with which it is annotated.
-Rendering speed has been improved by disabling anti-aliasing via
- the Smooth Fonts
- option in the View
- menu (its default set in Preferences). In addition, response
- times when editing alignments can be reduced by turning off the automatic
- calculation of amino acid property Consensus (which has been
- reintroduced to the Calculate menu as Autocalculate Consensus).
-
Issues Resolved
-See the Release History page for details of all - new features and resolved issues.
- - + + + ++ 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. +
+