For an assignment I must do a pairwise optimal local alignment using BLOSUM65 and five protein sequences. The algorithm I want to use is the Smith-Waterman.
Context protein sequencing using Blastp: all the sequences are the hemoglobulin subunit a or b;
- two times two pairs are from the same organism (but differ in subunit),
- one is not;
- all the sequences differ in sequence length (around ~15 amino acids. Gaps!)
The default for the BLOSUM65 penalties are: 10 for a gap, 1 for an extension.
How do I optimise the gap penalty and gap extension penalty? Should I stick with the default? If so, why?