I'm working on a project for a Coursera course where I need to scan a string of base pairs and identify possible genes, but there's something about real DNA that I need to know to design the algorithm correctly. My question is best illustrated by example.
Suppose we have a strand of DNA like this : ATGxxxyyyzzzTAAqqATGrsssATGuuTAAvpppTAG
The lower case letters just stand for general base pairs that are not in the sequences "ATG", "TAA", "TAG", or "TGA".
"ATGxxxyyyzzzTAA" constitutes a gene for the purposes of the assignment, and my program does correctly identify that string of base pairs as a gene. What I want to know focuses on what happens after that first gene is found. Let's consider the last portion of the string:
My current gene-finding program would identify "ATGrsssATGuuTAA" as a gene, but notice that this strand starts after only two base-pairs ("qq") have been searched through. Does that matter? I.e., would this happen in real DNA, or should the second valid gene be identified as "ATGuuTAAvpppTAG"?