[Bio-srs] Question about amino acid substitution matrices

Steffen Fehrmann Kasymir at gmx.net
Tue Aug 23 12:50:17 EST 2005


I'm a student of biology and one of my main focuses is bioinformatics.
At the moment I'm preparing for my final exam.
I read about that there are different bit units in different amino acid
substitution matrices, e.g. the BLOSUM62 Matrix, which is scaled in 1/2
bit units or the PAM 250, in 1/3 bits (Bioinformatics, Mount, D.W.). I
wouldn't care but gap penalty scores depend on these scales.
Despite I read how these matrices are generated, I didn't find a
description about the differences between 1/2 and 1/3 scaled aa
substitution matrices. So, what does that mean and how do the matrices
I hope anyone could help me and thank you for trying,


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