Is this sufficient? 

#!/usr/bin/perl
use strict;
use warnings;

my(@codons)= qw(ATG GTG);
my $dna = "AAAATGGGGTAAGTGAACGGGTAA";

my $splitter= join('|', @codons);

my @sequences= split /($splitter)/,$dna;
shift @sequences;

my $codon= 1;
foreach (@sequences) {
    if ($codon) {
        print $_,"-";
    }
    else {
        print $_,"\n"
    }
    $codon= not $codon;
}

[download]

output 

ATG-GGGTAA
GTG-AACGGGTAA

[download]

it works by splitting at codons, but capturing them. Then discarding the first (possibly empty) ouput of split and putting together every two elements of split's output.

s$$([},&%#}/&/]+}%&{})*;#$&&s&&$^X.($'^"%]=\&(|?*{%
+.+=%;.#_}\&"^"-+%*).}%:##%}={~=~:.")&e&&s""`$''`"e

In reply to Re: Orf subsequences by Skeeve
in thread Orf subsequences by odegbon

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