This Perl 5 program takes DNA as input and returns either a list of ORFs or a fplot formatted list of stop codons. The program reads a DNA seq. from standard input, and returns a list of ORFs longer than the minimum length set by the -o switch. If -o is not set, the default is 100 aa. Output is written to standard output.
Usage: orf [-f -o# -s[Start_bp,End_bp] ] <Dna.seq
-f Write list of stop codons in fplot format.
-o# This sets the minimum length a ORF has to be to get reported.
-sStart_bp,Stop_bp Only ORFs within the given bp range will be reported.
Example: orf <DNA.seq >orf.list orf -o50 <DNA.seq >orf.list
Last modified 1/27/96.
Written by Jim Lund in the lab of Roger Reeves, Johns Hopkins University