GP and Arka -- software for molecular biology

January Weiner nospam_jweiner1 at ix.urz.uni-heidelberg.de
Mon Feb 12 21:49:55 EST 2001


Hello.

	I have created two lightweight, Unix (or, rather, Linux) -based
	packages for manipulation / analysis of sequence data. Maybe
	someone is interested -- they were mainly for my own work, but they
	are pretty well documented and have certain advantages over GCG or
	GUI based software.

	"GP" is a set of small, command line tools written in portable ANSI
	C. I found it hard to analyse hundreds of sequences using GUI tools
	like DNA-star, so during the 3+ years of my Ph.D. I wrote a dozen
	or so small utilities for doing basic operations -- e.g. converting
	DNA to protein sequence, codon usage analysis, GC distros,
	resctriction site analysis, finding patterns, determining the Tm's
	of primers, quick search for conserved sequences and more. They are
	all written in a fashion that allows piping data to and through
	them, so you can glue them with standard Unix tools like awk, sed
	and co. Basically, there are better and more powerfull tools out
	there, but GP are smaller and usually quicker. And easier to
	install. 

	"Arka" is a graphical interface for those command line tools. It
	sounds stupid, first to create command line tools, and then to
	create a GUI for them. However, Arka is rather a graphical shell
	allowing you to issue virtually any command on your system.
	Besides, it has one or two features for which you just need GUI,
	like displaying 3D data.

	Arka is not as portable as "GP", but should install smoothly at
	least on most Linux systems.

	All programs are, as I said, lightweighed, which means running
	quickly on old machines (my laptop is a 486). Installation using
	rpm should be very easy, and the programs do not take much space.
	Besides, they are open sourced, so you if you need some starting
	point in creating own programs, this might be useful (I tried to
	make the code understandable and commented). If you think you could
	use something like that, go ahead. 

	Ah yes, the address: http://www.bioinformatics.org/genpak/
	You will find binary and source packages. I will be grateful for
	any comments.

	Best regards,
	j.

-- 
----)-\//-///-----------------------------------January-Weiner-3-------
Optimism about the future is always desirable; 
it may help to create a self-fulfilling prophecy - Sir Arthur Clarke







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