Question

Which of the following is untrue about Bayes Aligner?

(a) Posterior probability values, which are considered estimates of the true alignment, are calculated for each alignment

(b) The method generates a single best alignment

(c) It aligns two sequences using a Bayesian algorithm which is a unique sequence alignment method

(d) It is a web-based footprinting program

The question was asked in an internship interview.

My question is based upon Prediction Algorithms in portion Promoter and Regulatory Element Prediction of Bioinformatics

Answer 1

Correct option is (b) The method generates a single best alignment

Easiest explanation: Instead of returning a single best alignment, the method generates a distribution of a large number of alignments using a full range of scoring matrices and gap penalties. By studying the distribution, the alignment that has the highest likelihood score, which is in the extreme margin of the distribution, is chosen. Based on this unique alignment searching algorithm, weakly conserved motifs can be identified with high probability scores.