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gp_randseq
Langue: en
Version: 111689 (mandriva - 01/05/08)
Section: 1 (Commandes utilisateur)
NAME
gp_randseq - generate random DNA sequences from a master sequenceSYNOPSIS
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>
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre