>-- 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
>composition.
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
5=Nothing
Regards,
David Mathog
mathog at seqaxp.bio.caltech.edu
Manager, sequence analysis facility, biology division, Caltech
