# gp_mkmtx

## GP

## 2000

## 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_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>