What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwhatsNew.html;h=2533c8afc05ddfb386ddecddce9b54fdb113f504;hb=b6a1449403a84599e9b74f74fde14522c3ad62ea;hp=5bb50f9eb0e177707442c3bc1fd76fad58414dc2;hpb=20bddfcf8ef1a53bce455b7599f8066b8ccba0d4;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 5bb50f9..2533c8a 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,28 +1,87 @@ - -What's new ? - -

What's new ?

Jalview Version 2.1

The multiple sequence alignment program MAFFT - is available from the default Web Service list.

The sequence feature retrieval system using DBFetch from EBI has been replaced - with DAS Feature fetching capabilities.

Hide sequences and columns

Export Annotations and Features

GFF file reading / writing

Associate structures with sequences from local PDB files

Add sequences to exisiting alignment

Recently opened files / URL lists

Applet can launch the full application

Applet has transparency for features (Java 1.2 required)

Applet has user defined colours parameter

Issues Resolved

Redundancy Panel reinstalled in the Applet

Monospaced font - EPS / rescaling bug fixed

Annotation files with sequence references bug fixed

See the Release History page for details of all - new features and resolved issues.

- - + + + +What's new ? + + +

+ What's new ? +

+ 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. +

+ 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.

+ + +