Question

A method of sequence alignment based on a Model (Bishop and Thompson 1986) was introduced that predicts the manner in which DNA sequences change during evolution. Which of the following is wrong about it?

(a) This method is different from the Smith-Waterman local alignment algorithm

(b) This method is quite similar to the Smith-Waterman local alignment algorithm

(c) The underlying mutational theory is like those used to produce the PAM matrices for predicting changes in DNA and protein sequences

(d) Sequences are predicted to change by a Markov process such that each mutation in the sequence is independent of previous mutations at that site or at other sites

The question was asked in semester exam.

This key question is from The Maximum Likelihood Approach in portion Phylogenetic Tree Construction Methods and Programs of Bioinformatics

Answer 1

Correct option is (b) This method is quite similar to the Smith-Waterman local alignment algorithm

The best I can explain: This method is different from the Smith-Waterman local alignment algorithm in identifying the most probable (maximum likelihood probability alignment) based on an evolutionary model of change in sequences, as opposed to a score based on observed substitutions in related proteins and a gap scoring system. An example for option d can be–a given nucleotide at any sequence position can mutate into another at the same rate or may not change at all during a period of evolutionary time.