3 Weight Matrices for Sequence Similarity Scoring

This section is available here. A Postscript Version of it is available here.

Some Exercises involving Weight Matrices

(Author: Georg Fuellen. Further exercises are planned.)

1. 1. Why does 2 PAM, i.e. 1 PAM multiplied with itself, not correspond to exactly 2% of the amino acids having mutated, but a little less than 2% ? Or, in other words, why does a 250 PAM matrix not correspond to 250% accepted mutations ?

2. Is it biologically plausible that the C-C and W-W entries in the matrix are the most prominent ? Which entries (or groups of entries) are the least prominent ?

3. Why do some people talk about the 256 PAM matrix, and not the 250 PAM matrix ? What's so special about the value 256 ?

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