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gp_dimer

Langue: en

Version: 111680 (mandriva - 01/05/08)

Section: 1 (Commandes utilisateur)

NAME

gp_dimer - computate frequencies of nucleotide dimers

SYNOPSIS

[-H] [-q] [-v] [-d] [-h] [inputfile] [outputfile]

OPTIONS

-l
distance between the two nucleotides in base pairs. Default 0.
-H
Output in HTML mode
-v
Prints the version information.
-q
Do not display error messages
-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

gp_dimer records dinucleotide frequencies: in the simplest case -- frequencies of dimeres AA, AC, AG... ...TT. This is sometimes useful to characterize a sequence. You can also use it to see, what is the probability of finding a certain nucleotide N bases after another one, for example -- what is the frequency of an 'A' coming seven nucleotides after a 'T'. To set this distance, use the option -l.

SEE ALSO

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

ENTRAVES

M : En fait, on est plus limités par les capacités de notre cerveau que par une laisse...
P : Et c'est en cela qu'on est assez proches des intellectuels français...