Modeller Users Group,

I have two protein sequences. They have already been aligned and the lengths are identical . I have a few gaps in the alignment.

How do I calculate the percent similarity or percent identity between the two sequences. I know I need to use something like the BLOSUM50 or some other substitution matrix (for similarity).

How exactly do I do the math so that I end up saying "protein A and protein B are 70 % similar and 40 % identical".

Please note - I want to know how to do the math, step-by-step. I am not interested in using a computer program at this point, even if it is free, because I want to write my own code, once I understand how to do the math.

I have looked in several books, looked all over the Internet, BioPERL, etc, but I can not find a clear step-by-step explanation of how to do the math.

I would be most grateful if someone knowledgeable could explain this.

Thank you, Jim Metz

James T. Metz, Ph.D. Research Investigator Chemist

GPRD R46Y AP10-2 Abbott Laboratories 100 Abbott Park Road Abbott Park, IL 60064-6100 U.S.A.

Office (847) 936 - 0441 FAX (847) 935 - 0548

james.metz@abbott.com

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