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GP and Arka are very leightweighed programs for manipulation of DNA / RNA / protein sequences. They are designed on one hand to run smoothly on older machines, and on the other -- to faciliate processing of large numbers of sequence / data files. GP includes utilities to convert DNA / RNA to protein, determine codon usage / GC contents, promotor searches, Tm, searching for restriction sites, converting sequences into numerical representations and much more.
GP
GP is a set of small utilities written in ANSI C to manipulate DNA
sequences in a Unix fashion, fit for combining within shell and cgi
scripts. I
have done this utilities for myself and found them very useful for my work;
they are fast and quite reliable, and playing with large numbers of
sequences is much more convenient with command line interface then with standard
GUI tools. Feel free to mail me bug reports and suggestions. The programs are
supposed to compile fine under any ANSI C compiler, but I never tried any
platform other then Unix / Linux. You will find more details online on the GP man pages. And here is an example of a
site using GP programs in CGI scripts to do promoter searches on-the-fly.
Try out the
Oligo
calculator, a simple CGI script using the programs gp_tm and gp_primer.
The GP package contains many command-line utilities which fullfill a whole bunch
of tasks (from DNA sequence searches to restriction analysis and determining the
melting temperature of oligonucleotides). While those programs are convenient to
use in batch processing and CGI scripts (which was the purpose of those
programs), they lack a nice GUI.
Arka remembers the options for the GP programs and knows what both the programs
and the options do. Besides, it has some gadgets on its own. It requires GTK+,
but doesn't need GNOME. Also, it is small and quick: look, I write and use my
programs on an old 486 laptop. It should run like hot butter on your computer.
Unless, of course, it is a 386 SX.
The name comes from the "UAG" stop codon, which is traditionally called "arka
codon".
Arka
Arka is a program that (1) serves as a graphical interface for the programs
from the GP package (2) has some interesting funtions on it's one. Main scope of
the program is the manipulation and visualisation of DNA / RNA / protein sequences.
Download
GP
Source + i386 binaries, tar and gzipped:
gp-0.26.tgz
RPM, i386 binaries:
gp-0.26-1.i386.rpm
RPM, source:
gp-0.26-1.src.rpm
Arka
Source + i386 binaries, tar and gzipped:
arka-0.11.tgz
RPM, i386 binaries:
arka-0.11-1.i386.rpm
RPM, source:
arka-0.11-1.src.rpm
All files in the download directory
Changes
Debian packages
Debian packages are kindly provided by Fatih Demir. You can find them on www.kabalak.net.PowerPC binaries
PowerPC RPMs can be found on www.linuxppc.org. Thanks to Eric Marston!To run arka, you will also need glibc, gdk and gtk. Most probably, if
you are using a standard Linux distribution, you already have them (and you
definitely do if you are using GNOME or GIMP). If not, check www.gtk.org.
My e-mail address is january@bioinformatics.org. Feel free to
contact me any time.
Contact