Protein distance/similarity measure

mathog at mathog at
Wed May 20 10:41:37 EST 1998

>-- 	I am in need of a program to calculate pairwise 
>similarity scores between amino acid sequences.  I need the
>score to be in the form of % similarity.

Do you have GCG?  You might try, for instance, OLDDISTANCES, or even the first
(pairwise) phase of PILEUP.

>	PIMA is the closest I can find to what I want.  But
>it gives a score that is dependent on the sequence length and

You can fix the latter part of this in pretty much all GCG programs by
using the appropriate comparison matrix.  As for length - well, that's
fundamental - any cumulative similarity/identity measurement will go up
with length. OLDDISTANCES lets you correct for this to some extent by
dividing the score by: 

                     1=length of the shorter sequence
                     2=length of the shorter sequence without gaps
                     3=Average length
                     4=Average length without gaps


David Mathog
mathog at
Manager, sequence analysis facility, biology division, Caltech 

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