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gp_digest
Langue: en
Version: 111679 (mandriva - 01/05/08)
Section: 1 (Commandes utilisateur)
NAME
gp_digest - show restriction sites of a sequenceSYNOPSIS
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>
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre