Rechercher une page de manuel

Chercher une autre page de manuel:

gp_digest

Langue: en

Version: 111679 (mandriva - 01/05/08)

Section: 1 (Commandes utilisateur)

NAME

gp_digest - show restriction sites of a sequence

SYNOPSIS

gp_digest [-o type] [-e enzymfile] [-q] [-v] [-d] [-h] enzym [inputfile] [outputfile]

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

o
sequence gp_digested with some enzymes I know.

SEE ALSO

Genpak(1) gp_acc(1) gp_adjust(1) gp_cdndev(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)

DIAGNOSTICS

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 :-)

BUGS

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.

AUTHOR

January Weiner III <january@bioinformatics.org>

Quand on est trop bonne pâte, on risque de finir dans le pétrin.
-+- Pierre Dac -+-