Question

Which of the following is untrue regarding the progressive alignment method?

(a) The program also applies a weighting scheme to increase the reliability of aligning divergent sequences (sequences with less than 25% identity)

(b) The progress is done by down weighting redundant and closely related groups of sequences in the alignment by a certain factor

(c) This scheme is useful in enhancing similar sequences from dominating the alignment

(d) This scheme is useful in enhancing similar sequences from dominating the alignment

This question was addressed to me in exam.

Origin of the question is Heuristic Algorithms in chapter Multiple Sequence Alignment of Bioinformatics

Answer 1

The correct answer is (c) This scheme is useful in enhancing similar sequences from dominating the alignment

To explain: This scheme is useful in enhancing similar sequences from dominating the alignment. Further, the weight factor for each sequence is determined by its branch length on the guide tree. The branch lengths are normalized by how many times sequences share a basal branch from the root of the tree.