Question

Which of the following is untrue regarding Expectation Maximization algorithm?

(a) An initial guess is made as to the location and size of the site of interest in each of the sequences, and these parts of the sequence are aligned

(b) The alignment provides an estimate of the base or amino acid composition of each column in the site

(c) The column-by-column composition of the site already available is used to estimate the probability of finding the site at any position in each of the sequences

(d) The row-by-column composition of the site already available is used to estimate the probability

The question was asked during an interview.

Asked question is from Statistical Methods for Aiding Alignment topic in division Multiple Sequence Alignment of Bioinformatics

Answer 1

Correct choice is (d) The row-by-column composition of the site already available is used to estimate the probability

Easiest explanation: The EM algorithm then consists of two steps, which are repeated consecutively. In step 1, the expectation step, the column-by-column composition of the site already available is used to estimate the probability of finding the site at any position in each of the sequences. These probabilities are used in turn to provide new information as to the expected base or amino acid distribution for each column in the site.