Smith-Waterman

Implementation of Smith Waterman algorithm, used to perform local sequence alignment

Running the script

This script takes two sequences in .fasta format. It uses the BLOSUM62-matrix to determine match-scores, you need to have BLOSUM64.txt in the same directory wich you run the script from.

$ python3 Smith-Waterman.py <seq1.fasta> <seq2.fasta>