Arka is a simple graphical user interface for command line programs, with
the focus on the gp package of sequence analysis tools
(http://www.bioinformatics.org/genpak). The program reads a description of
the command line tools from a text file and produces a GUI dialog upon
users request. Then, the command line program is executed, and output /
error messages can be recorded and edited.
Together with the gp programs, it features:
* simple sequence searches
* promoter searches [*]
* codon usage analysis
* ORF searches and converting DNA sequences to protein sequences
* pattern frequency analyses
* converting DNA sequences to cross-correlated variable matrices
* Tm primer analysis
* analysis of primer secondary structures and dimeres
* simple restriction site analysis
* on-the-fly creation of PNG graphical gene maps
Changes in 0.06 include several bugfixes, full GUI editing and creation of
the specifications of the command line programs (you can, for example,
create easily a dialog for the blasta program family), and better job
Arka is written in C/ Gtk+, so it is mainly for Unix systems. It is quick,
small, does not depend on GNOME/KDE and is early beta :-). In theory, it could
serve as a GUI for any command line programs, from blasta to zip, it is
just a matter of creating a specification file.
Apart from being a user interface for other programs, there are two small
visualisation tools -- one for creating *very* primitive GC contents graphs
and one for fully interactive displaying 3D graphs (which I coded to
visualize some DNA structural features I was working on).
You'll find it on http://www.bioinformatics.org/genpak/. I am interested in
any comments on the programs usability. An example of using the gp programs
in CGI scripts can be found on
[*] using the Hertz matrix method, for details see Weiner, J., R. Herrmann
and G.F. Browning 2000, Nucleic Acids Res. 28:4488-96.
The art of flying is to throw yourself at the ground and miss.