Global Alignment with Constant Gap Penalty

Problem

In a constant gap penalty, every gap receives some predetermined constant penalty, regardless of its length. Thus, the insertion or deletion of 1000 contiguous symbols is penalized equally to that of a single symbol.

Given: Two protein strings s and t in FASTA format (each of length at most 1000 aa).

Return: The maximum alignment score between s and t. Use:

The BLOSUM62 scoring matrix.
Constant gap penalty equal to 5.