Question

The resulting tree is then used to guide the alignment of the most closely related sequences and groups of sequences. The resulting alignment is a global alignment produced by the Needleman-Wunsch algorithm.

(a) True

(b) False

I had been asked this question in an interview for job.

My question is from Progressive Methods of Multiple Sequence Alignment topic in portion Multiple Sequence Alignment of Bioinformatics

Answer 1

The correct answer is (a) True

The best explanation: The very first sequences to be aligned are the most closely related on the sequence tree. If these sequences align very well, there will be few errors in the initial alignments. However, the more distantly related these sequences, the more errors will be made, and these errors will be propagated to the MSA. There is no simple way to circumvent this problem. A second problem with the progressive alignment method is the choice of suitable scoring matrices and gap penalties that apply to the set of sequences.