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gp_primer

Langue: en

Version: 111687 (mandriva - 01/05/08)

Section: 1 (Commandes utilisateur)

NAME

gp_tm - calculate stem/loop and dimere structures of an oligonucleotide

SYNOPSIS

gp_tm [-m] [-q] [-v] [-d] [-h] [inputfile] [outputfile]

OPTIONS

-i
for each sequence, prints the sequence number, the dG values for the most stable dimere and the most stable stem/loop, and the sequence name, all fields separated by a TAB.
-m value
sets the maximal number of structures to be shown (default 5)
-v
Prints the version information.
-d
Prints lots of debugging information.
-h
Shows usage information.
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

SEE ALSO

Genpak(1) gp_acc(1) gp_adjust(1) gp_cdndev(1) gp_cusage(1) gp_digest(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_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>

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