gp_randseq(1)

NAME
gp_randseq - generate random DNA sequences from a master sequence

SYNOPSIS
gp_randseq [-l length] [-number] [-q] [-v] [-d] [-h] [inputfile] [outputfile]

OPTIONS

-n value
    set the number of random sequences to value

-l value
    set the random sequence length to value

-m  instead of cutting out sequences at random positions in the genome, computate the Markov chain probabilities for nucleotides and generate sequences basing on that.

-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_randseq cuts out random sequences from a larger sequence. It is useful in genomic comparisons (e.g. what will be the distribution of a certain parameter in my set of sequences as compared to random sequences). The probability distribution of the sequence start should be linear.

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_primer(1) gp_qs(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>