gp_findorf - print ORFs contained in a sequence
gp_findorf [-m value] [-M value] [-o option] [-c file] [-p type] [-q] [-v] [-d] [-h] [inputfile] [outputfile]
- -m value
- set the minimal considered ORF length to value bp.
- -M value
- set the maximal considered ORF length to value bp.
- 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
- print the codon table and exit
- -c code_file
- load codon table modifications from file code_file
- Prints the version information.
- Prints lots of debugging information.
- Shows usage information.
- file to proces; if not given, will use standard input
- file to write the data to; if not given, will
use standard output
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.
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
The Genpak programs do not write over existing files. I have found this
feature very useful :-)
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.
January Weiner III