I'm making a quick program to help me with another project. I need a program that takes two files, which will both be the DNA sequences of two separate viruses (I'm trying to isolate certain genes in viruses - I got a great idea for my doctoral thesis!), and then it goes through and look for 3 or more consecutive matching codes. For example, if I had:
TGACCGATTATTG
and
GATTCCCATCGCA,
the program would signal the GAT. It would function slightly different from this, but I'd have to explain the specifics of how cells code DNA/RNA into proteins. So could someone point me in the right direction for an algorithm that would do this kind of thing, and I could just do the appropraite changes. I've searched aihorizon.com and none of them seemed to help. I could probably write one, but it owuld be incredibly slow, so some of the ideas like theirs for search algorithms might help. Thanks for any advice you might be able to give, I appreciate it.
