gp_digest

GP

2000

NAME

SYNOPSIS

OPTIONS

-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 fragment

-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 fragments

-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.

-v

Prints the version information.

-d

Prints lots of debugging information.

-h

Shows usage information.

enzym

the enzyme you want to "gp_digest" your fragment with. Lowercase/ uppercase doesn't matter.

inputfile

file to proces; if not given, will use standard input

outputfile

file to write the data to; if not given, will use standard output

DESCRIPTION

gp_digest simulates a gp_digestion of a sequence fragment with a restriction enzyme.

EXAMPLES

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

NOTE

This program has not yet been thoroughfully checked, although it prints correct enzyme restriction sites for the