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gp_mkmtx

Langue: en

Version: 111685 (mandriva - 01/05/08)

Section: 1 (Commandes utilisateur)

NAME

gp_mkmtx - calculate frequencies of nucleotides

SYNOPSIS

gp_mkmtx [-a] [-g value] [-l] [-q] [-v] [-d] [-h] [inputfile] [outputfile]

OPTIONS

-a
print only the absolute numbers of occurencies
-g value
divide each frequency by the expected frequency at GC contents equal to value %.
-l
do not apply logarythmic scaling (as a default, gp_mkmtx calculates the logarythm of the frequencies.
-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

gp_mkmtx is supposed to be a tool for an easy creation of matrices for the gp_matrix program. It takes a set of sequences, calculates the frequency of a nucleotide at each position starting from the first nucleotide and ending with the last nucleotide of the shortest sequence. For each position, four values are printed in a row, respectively for A, C, G and T/U. Each value is the logarithm of the calculated frequency (logarythmisation can be suppresed with the -l option). If the -g option is used, prior to the logarithmic scaling the values are diveded by the expected frequency at the given GC contents (that is, for example, at GC=50%, 0.25 for each nucleotide).

EXAMPLES

gp_mkmtx -g 50 somesequence.fasta somesequence.mtx

will produce a matrix file somesequence.mtx which, after some editing, will be directly suitable for the gp_matrix program.

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_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>

Faut rien bouger à votre système. Tout tourne comme avant, mais avec le
Multidesk, qui supporte la domotique, permet de réparer votre Windows
s'il tombe en panne, puisqu'il tient sur une disquette, etc... Pas
besoin de créer de partition, Windows croit que c'est un programme
-- Jayce - Attendez, je claque dans mes doigts --