[BiO BB] A qestion about BLOSUM matrices in Genedoc

Richard Cai xj_cai at yahoo.com
Thu Apr 29 12:51:35 EDT 2004

Hi there,

I recetly used Genedoc to align about 150 protein
sequences, and I found that there were
numbers/characters at the bottom of some of the
conserved residues, for example, p, a, 1, 6 or 7. I
chose the BLOSUM62 matirx.

What are these symbols for? My understanding was that
these positive numbers calculated by BLOSUM suggested
better local similarity. But why no numbers were shown
for other conserved residues? How about "p" and "a".
Do they stand for amino acid "Pro" or "Ala"? Thanks a

Richard Cai
Dept. of Cardiovascular Sciences
University of Calgary, Canada

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