gp_digest - show restriction sites of a sequence
gp_digest [-o type] [-e enzymfile] [-q] [-v] [-d] [-h] enzym [inputfile] [outputfile]
- -o type
- Output type. Following types are accepted (it is
enough to give the first letter):
- -o ascii
- (default) draws a simple ascii scheme of the restricted
- -o position
- prints restriction sites, which are always the 5'
ends of the plus strang
- -o sequences
- simulates gp_digestion of a given sequence and prints
out the fragments which will be left after gp_digestion, from the 5'
to the 5' end (sometimes the 3' ends will be longer!)
- -o fragments
- prints the positions from the abovementioned
- -o lengths
- print only the lengths of the gp_digested fragments
- -o number
- shows only a total number of gp_digested fragments
- -e enzymfile
- takes the enzyme descriptions from the specified
enzyme file. The default file is defined at the compilation time,
usually it is /usr/lib/genpak/enzyme.enz, which contains most of the
known restriction enzymes. You can copy it to your local directory and
modify to suit your needs.
- Prints the version information.
- Prints lots of debugging information.
- Shows usage information.
- the enzyme you want to "gp_digest" your fragment with.
Lowercase/ uppercase doesn't matter.
- file to proces; if not given, will use standard input
- file to write the data to; if not given, will
use standard output
gp_digest simulates a gp_digestion of a sequence fragment with a
To simulate what you will see on a gel after a gp_digestion with two
enzymes, do something like that:
gp_digest -o s AflII yoursequence | gp_digest -o n EcoRI | sort -n +0
This program has not yet been thoroughfully checked, although it prints
correct enzyme restriction sites for the sequence
gp_digested with some enzymes I know.
All Genpak programs complain in situations you would also complain,
like when they cannot find a sequence you gave them or the sequence is not
The Genpak programs do not write over existing files. I have found this
feature very useful :-)
I'm sure there are plenty left, so please mail me if you find them. I tried
to clean up every bug I could find.
January Weiner III