Implementing the Smith-Waterman algorithm in Python
https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm
"The Smith–Waterman algorithm performs local sequence alignment; that is, for determining similar regions between two strings of nucleic acid sequences or protein sequences. Instead of looking at the entire sequence, the Smith–Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure."
Usage :
- You can define the two sequences to be aligned at the beginning of the code
- This program supports affine penalties for gap : simply define the gap penalty in the function at the very end of the script
- Run the code, it displays the substitution matrix and the alignement, along with a couple stats
ℹ️ Please report any bug/issue in the issues section or directly at sebcararo@hotmail.fr. Any feedback is really appreciated 💬 👍.