You down with OOP...

[nkuipers]

>Incidentally, how much data do you expect to end up storing in one of
>these objects, and how many instances per execution?

I am not sure but I think that as a simple object, description and sequence is 
sufficient, because they are all that is required for biologically relevant 
operations like masking all occurences of a certain substring, producing the 
[reverse] complement of the sequence, getting the sequence length, comparing 
to other sequences, and so forth.  I am guessing there would be a severe 
bottleneck though if I used this in my real work...I typically deal with over 
15,000 sequences at a time.  Now, I could always populate an array (or 
something) with objects and wield them en masse, but the overhead of 15,000+ 
objects, even if they were small like the little driver I showed, would be 
significant perhaps?

Nathanael