Question

Which of the following does not describe PAM matrices?

(a) These matrices are used in optimal alignment scoring

(b) It stands for Point Altered Mutations

(c) It stands for Point Accepted Mutations

(d) It was first developed by Margaret Dayhoff

The question was asked during an interview.

My enquiry is from Global Sequence Alignment in section Sequence Alignment of Bioinformatics

Answer 1

Correct option is (b) It stands for Point Altered Mutations

To explain I would say: PAM stands for Point Accepted Mutations. PAM matrices are calculated by observing the differences in closely related proteins. One PAM unit (PAM1) specifies one accepted point mutation per 100 amino acid residues, i.e. 1% change and 99% remains as such.