[modeller_usage] How to calculate amino acid similarity and identity

[James T Metz <>]

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



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