Question

Which of the following is not a drawback of the progressive alignment method?

(a) The progressive alignment method is not suitable for comparing sequences of different lengths because it is a global alignment–based method

(b) In this method the use of affine gap penalties, long gaps are not allowed, and, in some cases, this may limit the accuracy of the method

(c) In this method the use of affine gap penalties, long gaps is allowed, and, in some cases, this may limit the accuracy of the method

(d) The final alignment result is also influenced by the order of sequence addition

This question was posed to me in homework.

My query is from Heuristic Algorithms in section Multiple Sequence Alignment of Bioinformatics

Answer 1

Correct choice is (c) In this method the use of affine gap penalties, long gaps is allowed, and, in some cases, this may limit the accuracy of the method

To explain I would say: Another major limitation is the “greedy” nature of the algorithm: it depends on initial pair wise alignment. Once gaps introduced in the early steps of alignment, they are fixed. The final alignment could be far from optimal. The problem can be more glaring when dealing with divergent sequences.