Question

Which of the following is incorrect regarding the ab initio approaches?

(a) The conventional approach to detecting a promoter or regulatory site is through matching a consensus sequence pattern represented by regular expressions

(b) The conventional approach to detecting a promoter or regulatory site is through matching a position-specific scoring matrix constructed from well-characterized binding sites

(c) The consensus sequences or the matrices are relatively short, covering 6 to 10 bases

(d) The consensus sequences or the matrices are relatively large, covering 700 to 1000 bases

The question was asked during an interview for a job.

My doubt stems from Prediction Algorithms topic in portion Promoter and Regulatory Element Prediction of Bioinformatics

Answer 1

Right option is (d) The consensus sequences or the matrices are relatively large, covering 700 to 1000 bases

Easiest explanation: To determine whether a query sequence matches a weight matrix, the sequence is scanned through the matrix. Scores of matches and mismatches at all matrix positions are summed up to give a log odds score, which is then evaluated for statistical significance. This simple approach, however, often has difficulty differentiating true promoters from random sequence matches and generates high rates of false positives as a result.