I am usually a Python / Database programmer, and I am considering using C for a problem.

I have a set of sequences, 8 characters long with 4 possible characters. My problem involves combining sets of these sequences and filtering which sets match a criteria. The combinations of 5 run into billions of rows and takes around an hour to run.

So I can represent each sequence as 2 bytes.

If I am working on a 64 bit architechture will I gain any advantage by keeping these data structures as 2 bytes when I generate the combinations, or will I be as well storing them as 8 bytes / double ? (64 bit = 8 x 8)

If I am on a 64 bit architecture, all registers will be 64 bit, so in terms of operations that shouldn´t be any faster (please correct me if I am wrong).

Will I gain anything from the smaller storage requirements - can I fit more combinations in memory, or will they all take up 64 bits anyway?

And finally, am I likley to gain anything coding in C. I have a first version, which stores the sequence as a small int in a MySQL database. It then self joins the tabe to itself a number of times in order to generate all the possible combinations. The performance is acceptable, depending on how many combinations are generated. I assume the database must involve some overhead.