Thanks guys for all the code...it will take some time go through it all...being a bit of a newbie and all
The answer to your last question tfrayner is that I would like to have a minimum of 3 residues that match...hopefully more of course

I was avoiding these more biological type details so that they would not confuse the issue for some.

You basically have it right...imagine the user desiring to take his/her "motif" (lets say 10 a.a.) and searching it against one or more protein sequences. The program must match any part, and as much of, the initial input as possible to the protein sequence(s). All cases where there is any type of a match must be printed out.
Hope this clarifies more of what I am trying to do. I notice that you are a post doc...cool...I am part of a research team at the Clinical Genomics Centre in Toronto, Canada.

Thanks again for your help, it is greatly appreciated!
dr_jgbn