Question

Which of the following is incorrect regarding PRRP?

(a) The program PRRP uses iterative methods to produce an alignment

(b) An initial pair-wise alignment is made to predict a tree

(c) Only one cycle is performed

(d) The whole process is repeated until there is no further increase in the alignment score

This question was posed to me in an interview for internship.

Query is from Iterative Methods of Multiple Sequence Alignment in chapter Multiple Sequence Alignment of Bioinformatics

Answer 1

The correct answer is (c) Only one cycle is performed

To explain: As mentioned, an initial pair-wise alignment is made to predict a tree, the tree is used to produce weights for making alignments in the same manner as MSA except that the sequences are analyzed for the presence of aligned regions that include gaps rather than being globally aligned, and these regions are iteratively recalculated to improve the alignment score. The best scoring alignment is then used in a new cycle of calculations to predict a new tree, new weights, and new alignments.