Question

In EM algorithm, as an example, suppose that there are 10 DNA sequences having very little similarity with each other, each about 100 nucleotides long and thought to contain a binding site near the middle 20 residues, based on biochemical and genetic evidence. the following steps would be used by the EM algorithm to find the most probable location of the binding sites in each of the ______ sequences.

(a) 30

(b) 10

(c) 25

(d) 20

I have been asked this question in an interview for internship.

This interesting question is from Statistical Methods for Aiding Alignment in section Multiple Sequence Alignment of Bioinformatics

Answer 1

The correct choice is (b) 10

The explanation is: When examining the EM program MEME, the size and number of binding sites, the location in each sequence, and whether or not the site is present in each sequence do not necessarily have to be known. For the present example, the following steps would be used by the EM algorithm to find the most probable location of the binding sites in each of the 10 sequences.