X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwhatsNew.html;h=d1d141d30b133f0a400e7fb369ebe9cce029c4d5;hb=8333f7266bd69f387a8c9c09cb844b615856a626;hp=693b0f0227b0a41f5ecfc8f9f9977c25fd0f8169;hpb=a5a0d509e08a0b6db7fd92a14006b7a3f2be22cf;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 693b0f0..d1d141d 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,64 +24,55 @@

- What's new ? + What's new in Jalview 2.10.1 ?

- 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. + Jalview 2.10.1 was released on 29th November 2016. Full details are + in the Jalview 2.10.1 + Release Notes, but the highlights are below. This is also the + first release to include contributions from Kira Mourão, who + joined Jalview's core development team in October 2016.

- 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.
More memory efficient
We've slimmed + down the consensus analysis data structures used by Jalview so + even wider alignments can be worked with.
Select highlighted region
Press 'B' + or use the new menu option in the alignment window's Select menu + to mark columns containing highlighted regions generated from + structure selections, mouse-overs, or resulting from a Find + operation.
New custom link mechanism for opening URLs + for database cross references.
If you have customised URL + links in your Jalview preferences, then you may already have seen + the warning dialog (see below).
New command line export option for BioJS + MSAviewer
A number of small bugs with the HTML export + functions from the Jalview desktop were also fixed.
Small but significant changes to the + physicochemical properties and consensus calculations
Threonine + is no longer considered a non-hydrophobic residue in the protein + conservation calculation, and minor bugs addressed in PID and + consensus colouring.
Correct display of disulphide bond + features
In linked structure views, Jalview would + highlight all residues between in addition to the two linked + cysteines. The 'select columns by feature' function in the feature + settings would also select all intermediate columns.

+ Warning dialog about updating + your configured URL links
In the desktop prior to Jalview + 2.10.1, the only way to configure custom links for a particular + database cross-reference for a sequence was to give it a name that exactly + matched the database source, and a regular expression for filtering + out any spurious matches generated when the custom linked was tested + against the Sequence's ID string. Since the introduction of the + $DB_ACCESSION$ token, however, $SEQUENCE_ID$ will not be used for + database cross-reference accession strings, and if you have custom + links configured, Jalview will raise a warning message so let you + know that you may need to update your links to use $DB_ACCESSION$. +