X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwhatsNew.html;h=d92f26b9018aa57315abaaa5469aba8f1d7c06c1;hb=ecdbc96815298ac853543640881ef8d2384b48a1;hp=04fcc6983b3836269a2dd43571edf3aa744404a3;hpb=11d7be472ca5ea89d69e5bb7882c0058b2c3c4b9;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 04fcc69..d92f26b 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,62 +24,37 @@

- What's new ? + What's new in Jalview 2.10.3 ?

- 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. + Version 2.10.3 was released in November 2017. The full list of + bug fixes and new features can be found in the 2.10.3 Release Notes, but + the highlights are below.

Faster import and more responsive UI when working with wide alignments and handling hundreds and thousands of sequence features
+
Improved usability with PDB and + UniProt Free Text Search + dialog, and new tab for retrieval of sequences for lists of IDs.
Short names assigned to sequences retrieved from UniProt

- Highlights in Jalview 2.9 + Experimental Features +

+ This release of Jalview introduces an Experimental Features + option in the Jalview Desktop's Tools menu that allows you + to try out features that are still in development. To access the + experimental features below - 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 JPred4Jalview 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 mode 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.