Thank you guys. I really appreciate it.
I have also been looking for how to implement this algorithm:The Smith-Waterman algorithm is a well-known algorithm for performing local sequence alignment; that is, for determining similar regions between two nucleotide or protein sequences. Instead of looking at the total sequence, the Smith-Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure.
I want to search a FASTA format file in a data base. Any reference will be good. I know the biology, i just cant put it in c++!!