Question

Which of the following is untrue about PRRN?

(a) PRRN is a web-based program that uses a double nested iterative strategy for multiple alignment

(b) It performs multiple alignments through two sets of iterations: inner iteration and outer iteration

(c) In the outer iteration, an initial random alignment is generated that is used to derive a UPGMA tree

(d) In the inner iteration, the sequences are randomly divided into multiple groups

I have been asked this question during an internship interview.

I would like to ask this question from Heuristic Algorithms topic in chapter Multiple Sequence Alignment of Bioinformatics

Answer 1

Right answer is (d) In the inner iteration, the sequences are randomly divided into multiple groups

To explain: In the inner iteration, the sequences are randomly divided into two groups. Randomized alignment is used for each group in the initial cycle, after which the alignment positions in each group are fixed. The two groups, each treated as a single sequence, are then aligned to each other using global dynamic programming. The process is repeated through many cycles until the total SP score no longer increases. At this point, the resulting alignment is used to construct a new UPGMA tree.