From Global to Local Alignment

Global alignment

You should now be ready to modify the alignment graph to solve a generalized form of the alignment problem that takes a scoring matrix as input.

Global Alignment Problem

Problem overview:
Find the highest-scoring alignment of two strings as defined by a scoring matrix.

Input: Two strings and a scoring matrix Score.
Output: An alignment of the strings whose alignment score (as defined by Score) is maximized among all possible alignments of the strings.