GP and Arka -- software for molecular biology
nospam_jweiner1 at ix.urz.uni-heidelberg.de
Fri Feb 9 10:00:17 EST 2001
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
"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
P.S. Hope this falls into the "methods" category :-P
Optimism about the future is always desirable;
it may help to create a self-fulfilling prophecy - Sir Arthur Clarke
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