gp_randseq
GP
2000
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_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>