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.
Return: The maximum local alignment score of
If multiple solutions exist, then you may output any one.
>Rosalind_8 PLEASANTLY >Rosalind_18 MEANLY
12 LEAS MEAN