What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=17ac27510659f2b4c483dd02eaf7b4a83cbd79c5;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=79cf7c98197d9c18e8884964fbeb4c5d7f93cc17;hpb=8a3915baf2a22618346a5a2ecd38f7fbca5d4a44;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 79cf7c9..17ac275 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,72 +1,87 @@ + --> What's new ? -

- What's new ?
Jalview 2.8.0b1 is a bugfix - release for Jalview version 2.8.
As usual you can find the - highlights below, and the comprehensive list is given in the Jalview 2.8.0b1 Release Notes. -

- This bug fix release includes numerous minor enhancements made over - the last 12 months. Importantly, it is also the first release that - provides Jalview as a trusted application, signed with a certificate - donated to us by Certum. + What's new ?

- Enhancements and new features -

Allow disorder predictions to be made on the current - selection (or visible selection) in the same way that JPred works
allow import of data from gzipped files
Improved per-sequence 'colour-by-annotation' performance
Support '' style escaping of quotes in Newick files
group options for JABAWS service by command line name
Select primary source when selecting authority in database - fetcher GUI
COMBINE statement uses current SEQUENCE_REF and GROUP_REF - scope to group annotation rows
add .mfa to FASTA file extensions recognised by Jalview
groovy scripting for headless jalview operation
Output in Stockholm format

- Bug fixes -

Uniprot and PDB database cross-reference fetching works - properly
'View all structures' in the desktop is more reliable
Web services parameter dialog box shows the options enabled - for different presets
Interactive creation of RNA secondary structure works more - smoothly
Keyboard mode 'P' command jumps to the right place
Improved support for parsing database cross-references via - Stockholm and Rfam database
Improved semantics in annotation files for grouping - annotation rows associated with particular sequences and groups
More robust DNA->Amino acid translation
Improved Headless-mode operation for DAS annotation - retrieval, groovy script execution and alignment figure generation
annotation label tooltip text needs to be wrapped

+ Jalview 2.9.0b1 is a bug fix release for Jalview 2.9, which 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 patches since version 2.9 was release, see the + Jalview 2.9.0b1 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.