Re:Mmmm.. (Score 1)

I'm not sure if stop/start codons would even matter, as it's my understanding that when DNA is used as a computational tool, it is typically rather short, synthesized strands. Keep in mind that a stop/start codon is relevant once the DNA has been transcribed into RNA and the RNA is being translated into proteins - in other words, as far as the DNA is concerned a stop/start codon is just another three base pairs. Also, it's my understanding that besides looking at sequence for the result of the question asked, the ability of the DNA to form a number of 3D confirmations (hairpins, loops, etc) and the resulting thermodynamic properties of the structure are often the "output". As far as the orientation being important, it is -- within a single, given strand. That is what is so elegant about the way DNA works, you only need one strand to convey the necessary info. I meant orientation across strands, not within a single strand. The sequence within a single strand is of course crucial.