Question: A global alignment problem with affine gap penalty
gravatar for yokotze118
3.5 years ago by
yokotze1180 wrote:

If I am going to perform global alignment between FILRGF and QFIP by dynamic programming using affine gap penalty scheme, using BLOSUM62 soring matrix, gap penalty = 5+1(x-1), gap opening penalty = 5, gap extension penalty = 1.

How can I get -5 as th best score when aligning L to F?

ADD COMMENTlink modified 3.5 years ago by RamRS23k • written 3.5 years ago by yokotze1180

It is not clear what you are asking.

The scoring matrix and penalties will determine the alignment and hence the final alignment score. There is nothing else left to "adjust" or tune. Perhaps what you could change is how to score trailing gaps at the end but that would be quite the stretch and most tools only offer you the chance to include or not.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Istvan Albert ♦♦ 81k
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