Question

For what type of sequences Gibbs sampling is used?

(a) Closely related sequences

(b) Distinctly related sequences

(c) Distinctly related sequences that share common motifs

(d) Closely related sequences that share common motifs

This question was addressed to me in an online interview.

My doubt stems from Motif Discovery in Unaligned Sequences topic in section Sequence Alignment of Bioinformatics

Answer 1

The correct option is (c) Distinctly related sequences that share common motifs

For explanation I would say: Often, distantly related sequences that share common motifs cannot be readily aligned. For example, the sequences for the helix-turn-helix motif in transcription factors can be subtly different enough that traditional multiple sequence alignment approaches fail to generate a satisfactory answer. For detecting such subtle motifs, more sophisticated algorithms such as expectation maximization (EM) and Gibbs sampling are used.