What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=19be76f59844b47234a5a9550d2f6275656530d3;hb=a4ff95a8db54817a175579ba15c070dd74a2b650;hp=3ee853417fa61c56a24ae76c047d86536076d233;hpb=dbc8ffccfdd7ff6f028ef8496e168219bd49ec8a;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 3ee8534..19be76f 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,74 +1,88 @@ + --> What's new ? -

- 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. -

+ What's new ? +

+ Jalview 2.9.0b2 is a bug fix release for Jalview 2.9. + The release of Jalview 2.9 in September 2015 included + 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 patches since version 2.9 was released, see the + Jalview 2.9.0b2 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.