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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>

Contenus ©2006-2021 Benjamin Poulain

Design ©2006-2021 Maxime Vantorre