Alignment of profiles

[Dennis Livesay]

Hi,

I'm attempting to globally align two profiles.  I need to determine a score 
for the overall similarity between the two profiles that won't be biased by 
the size of the initial profiles.  Meaning, simply adding up the column scores 
from the final MSA won't suffice because the larger of the two initial 
profiles would have a larger influence on the final score.  Any help?

Thanks,
Dennis

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Dr. Dennis Livesay
Department of Chemistry
Cal Poly, Pomona
phone: 909-869-4409
email: drlivesay at csupomona.edu

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