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gp_findorf
Langue: en
Version: 111681 (mandriva - 01/05/08)
Section: 1 (Commandes utilisateur)
NAME
gp_findorf - print ORFs contained in a sequenceSYNOPSIS
gp_findorf [-m value] [-M value] [-o option] [-c file] [-p type] [-q] [-v] [-d] [-h] [inputfile] [outputfile]OPTIONS
- -m value
- set the minimal considered ORF length to value bp.
- -M value
- set the maximal considered ORF length to value bp.
- -o
- specify output type:
- -o s[equences]
- print the protein sequences of the ORFs.
- -o p[ositions]
- print the nucleotide positions of the ORFs in the sequence(s).
- -p
- print the codon table and exit
- -c code_file
- load codon table modifications from file code_file
- -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_findorf prints out all ORF it is able to retrieve from the provided sequence(s) in all six reading frames. gp_findorf always prints the longest ORF possible. ORF is defined as a nucleotide sequence starting with a start codon and ending with a stop codon; the sequences cannot be degenerated (obviously), but have to be strict DNA or RNA sequences.
See also gp_seq2prot(1) for additional details.
SEE ALSO
Genpak(1) gp_acc(1) gp_adjust(1) gp_cdndev(1) gp_cusage(1) gp_digest(1) gp_dimer(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_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 ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre