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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