X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwhatsNew.html;h=4b821794e06755ef60c7a2421b4b3faee15327d3;hb=f89f3ea0068a1be259c1705277eecf1614484616;hp=b115385f5db59c5a464ba9dc9a6d2f76268686c6;hpb=82bb69383ab22735cbd3440c670ae0b290fe6afd;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index b115385..4b82179 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,63 +24,52 @@

- What's new ? + What's new in Jalview 2.10.2 ?

- 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. + Full details about Jalview 2.10.2 are in the Release Notes, but the + highlights are below.

Update to JABAWS 2.2
Jalview's + alignment, protein conservation analysis, and protein disorder and + RNA secondary structure prediction services are now provided by JABAWS 2.2. + Several of the programs provided as services have been updated, so + their options and parameters have changed.
New preferences for opening + web pages for database cross-references via the UK Elixir's + EMBL-EBI's MIRIAM database and identifiers.org services. +
Showing and hiding regions +
- Hide + insertions in the PopUp menu has changed its behaviour. + Prior to 2.10.2, columns were only shown or hidden according + to gaps in the sequence under the popup menu. Now, only + columns that are gapped in all selected sequences as well as + the sequence under the popup menu are hidden, and column + visibility outside the selected region is left as is. This + makes it easy to filter insertions from the alignment view + (just select the region containing insertions to remove) + without affecting the rest of the hidden columns.

- Highlights in Jalview 2.9 + Experimental Features +

+ This release of Jalview includes a new option in the Jalview Desktop + that allows you to try out features that are still in development. + To access the features described below, please first enable the Tools→Enable + Experimental Features option, and then restart Jalview. +

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, and have IDs matching - 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 the ability 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.
Annotation transfer between Chimera and Jalview
Two + new entries in + the Chimera viewer's Chimera menu allow positional annotation to + be exchanged between Chimera and Jalview.