Question

The matrices PAM250 and BLOSUM62 contain _______

(a) positive and negative values

(b) positive values only

(c) negative values only

(d) neither positive nor negative values, just the percentage

I had been asked this question during an interview for a job.

My doubt stems from Dynamic Programming Algorithm for Sequence Alignment topic in section Sequence Alignment of Bioinformatics

Answer 1

Right choice is (a) positive and negative values

For explanation I would say: These matrices contain positive and negative values, reflecting the likelihood of each amino acid substitution in related proteins. Using these tables, an alignment of a sequential set of amino acid pairs with no gaps receives an overall score that is the sum of the positive and negative log odds scores for each individual amino acid pair in the alignment.