Question

Which of the following is incorrect regarding Cluster-Buster?

(a) It is an HMM-based web-based program

(b) A query sequence is scanned with a window size of 1 kb for putative regulatory motifs using motif HMMs

(c) It works by detecting a region of high concentration of unknown transcription factor binding sites and regulatory motifs at the initiation

(d) It is designed to find clusters of regulatory binding sites

I got this question by my school principal while I was bunking the class.

The doubt is from Prediction Algorithms topic in division Promoter and Regulatory Element Prediction of Bioinformatics

Answer 1

Right answer is (c) It works by detecting a region of high concentration of unknown transcription factor binding sites and regulatory motifs at the initiation

To explain: It works by detecting a region of high concentration of known transcription factor binding sites and regulatory motifs. If multiple motifs are detected within a window, a positive score is assigned to each motif found. The total score of the window is the sum of each motif score subtracting a gap penalty, which is proportional to the distances between motifs. If the score of a certain region is above a certain threshold, it is predicted to contain a regulatory cluster.