Arka 0.11 released

[January Weiner]

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:

(new)	* interfaces for the WU-BLAST and FASTA programs
	* sequence editor
	* simple sequence searches 
	* interface for various unix utilities (find, grep et co.)
	* 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
	
Changes in 0.11 include numerous bug fixes and interfaces for WU-BLAST and
FASTA programs.

Changes in 0.08 include reworked GP and unix program specifications, minor
bugfixes and configurable shortcuts for menu items.

Changes in 0.07 include many major bugfixes and a new utility -- a sequence
editor.

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) and a sequece
editor tool.

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
http://www.zmbh.uni-heidelberg.de/M_pneumoniae/Matrix .

Best regards,

January

[*] using the Hertz matrix method, for details see Weiner, J., R. Herrmann
and G.F. Browning 2000, Nucleic Acids Res. 28:4488-96.

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