July 2, 2012, midnight by Rosalind Team

**Topics**:
Alignment,
Dynamic Programming

## Building Upon Local Alignments

We have thus far worked with local alignments with a linear gap penalty and global alignments with affine gap penalties (see “Local Alignment with Scoring Matrix” and “Global Alignment with Scoring Matrix and Affine Gap Penalty”).

It is only natural to take the intersection of these two problems and find an optimal local alignment given an affine gap penalty.

Given: Two protein strings

Return: The maximum local alignment score of

- The BLOSUM62 scoring matrix.
- Gap opening penalty equal to 11.
- Gap extension penalty equal to 1.

If multiple solutions exist, then you may output any one.

>Rosalind_8 PLEASANTLY >Rosalind_18 MEANLY

12 LEAS MEAN