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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?

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  • $\begingroup$ I'm voting to close this question because it doesn't seem to have enough detail. Smith-Waterman is a well-known algorithm, the question is explicitly a homework question, but it's not clear from the question what form the answer should be in (e.g. what programming language). There's confusion because the question introduces BLASTp, which is a separate algorithm from Smith-Waterman. $\endgroup$ – gringer Jul 8 at 13:11