Thank you for pointing out my unclear question. What I mean by all DNA sequences I mean any coding region from the original DNA sequence, so anything that begins with a start codon (ATG) and ends with stop codon (TAG, TAA, or TGA). My problem is that some of these coding regions overlap in the original sequence so when I just try to match the sequence to the regex I only get one sequence, not the overlapping ones. There should be a total of 4 coding regions in the original sequence. I originally had tried changing my regex to ATG\w*T(AG|AA|GA) but I still get deep recursion. Wouldn't that regex just be matching the coding regions I want? When I got deep recursion, I tried changing my regex, but I see that I just made it match the entire string. Is the problem still with my regex or am I using recursion incorrectly?

In reply to Re^2: Using Recursion to Find DNA Sequences by clueless_perl
in thread Using Recursion to Find DNA Sequences by clueless_perl

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