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 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.

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 restriction enzyme.


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.


    Genpak(1) gp_acc(1) gp_cusage(1) gp_dimer(1) gp_findorf(1) gp_gc(1) gp_getseq(1) gp_map(1) gp_matrix(1) gp_mkmtx(1) gp_pattern(1) gp_primer(1) gp_qs(1) gp_randseq(1) gp_seq2prot(1) gp_slen(1) gp_tm(1) gp_trimer(1)


    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 valid.

    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 <>