Hello Sauoq,

I appreciate your helpful comments since I am not that savvy of a programmer. What led me to ask for help was the fact that I have to run approx. several million short sequences with lengths between 20 and 30 against the parent sequence file (known as the larger file), as well as the fact that I am actually in the middle of running approx. 100,000 of these short sequences through my basic program...it is still not finished after 3 weeks. So I feel compelled to improve things, otherwise my research on this topic will never get done.
Appreciate you help.

Dr.J