I have two strings A and B, let's say
A = AATCGGATATAG
B = CGATA
Some of you may know two types of alignments:
But I would like to implement an alignment that takes the best whole substring of A which, if aligned with B, yields the best alignment
For example:
A,B -- Alignment algorithm --> AATCGGATATAG
CG-ATA
So far I've been using the Smith-Waterman Algorithm
Does anyone know any suggestions to solve this problem?
Thanks in advance!