Question

Which of the following is untrue about the modification of PAM matrices?

(a) At one time, the PAM250 scoring matrix was modified in an attempt to improve the alignment obtained

(b) All scores for matching a particular amino acid were normalized to the same mean and standard deviation, and all amino acid identities were given the same score to provide an equal contribution for each amino acid in a sequence alignment

(c) This took place in 1976

(d) These modifications were included as the default matrices for the GCG sequence alignment programs in versions 8 and earlier and are optional in later versions

This question was addressed to me during an interview for a job.

My question comes from Use of Scoring Matrices and Gap Penalties in Sequence Alignments in section Sequence Alignment of Bioinformatics

Answer 1

The correct answer is:

(b) All scores for matching a particular amino acid were normalized to the same mean and standard deviation, and all amino acid identities were given the same score to provide an equal contribution for each amino acid in a sequence alignment

This statement is untrue. The PAM (Point Accepted Mutation) matrices, such as PAM250, are designed to represent evolutionary changes in protein sequences. They are not based on normalizing all scores to the same mean and standard deviation or giving equal scores to each amino acid identity. Instead, they assign different scores to each amino acid pair based on their likelihood of mutation during evolution. The matrix was not intended to equalize contributions from each amino acid but rather to reflect the probability of substitutions between amino acids over evolutionary time.

The other statements about the modification of PAM matrices (a, c, and d) are correct in historical and practical contexts.