Question

What is used to generate parameters for the extreme distribution?

(a) The pool of alignment scores from the shuffled sequences

(b) A single score of a shuffled sequence

(c) The pool of alignment scores from the unshuffled sequences

(d) The basic optimal score computed at the beginning of the test

This question was posed to me in a job interview.

My enquiry is from Statistical Significance of Sequence Alignment topic in portion Pairwise Sequence Alignment of Bioinformatics

Answer 1

The correct choice is (a) The pool of alignment scores from the shuffled sequences

To explain I would say: Maximum scores are obtained through repeated shuffling. Then the pool of alignment scores from the shuffled sequences is used to generate parameters for the extreme distribution. The original alignment score is then compared against the distribution of random alignments to determine whether the score is beyond random chance.