What's new ?

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwhatsNew.html;h=840b095d7fd22a60a85366619756da2d570d762e;hb=284d1b5c47c05ff1d34bbb8c88a7b76b84b969fb;hp=7bc6de4d46b346bf9999fdd9ccee266b31088471;hpb=1162b546d4804d709920737049d796a5a9aa71e1;p=jalview.git diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 7bc6de4..840b095 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,30 +1,88 @@ - -What's new ? - -

What's new ?

Jalview Version 2.07

Sequence Fetcher has been added to quickly - retrieve sequences with known ids from several databases.

Sequence Features enhanced to allow - the user to display all features of a Uniprot file on the alignment and subsequently - colour, hide or show overlapping features.

Choose to omit /start-end from sequences when - saving files. This is important for saving files to be used by some programs - which cannot read the original Jalview sequence output with the appended /start-end.

PDB structure viewer enhanced. Mapping - between sequence and structure has been enhanced, colours on the alignment are - reflected in the structure viewer.

Jalview Applet can read - in feature files, PDB files be used as input to HTML form See the website - to find out the new parameters available for the Applet Version of Jalview.

Issues Resolved

Group Editing is possible with Control and mouse click. Alt key and mouse press - does not work as this translates as the middle mouse button, which since 2.04 - is now used to scroll the alignment and change the font size.

HTML export now writes groups and features which were previously missing.

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

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

+ What's new ? +

+ Jalview 2.9.0b2 is a bug fix release for Jalview 2.9. + The release of Jalview 2.9 in September 2015 included + 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 released, see the + Jalview 2.9.0b2 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.

+ + +