Question

Which of the following is not a characteristic of exact matches in regular expression?

(a) There must be a strict match of sequence patterns

(b) Any variations in the query sequence from the predefined patterns are not allowed

(c) Provide more permissive matching by allowing more flexible matching of residues of similar biochemical properties

(d) Searching a motif database using this approach results in either a match or non-match

This question was posed to me in final exam.

My question is from Motif and Domain Databases Using Regular Expressions in portion Sequence Alignment of Bioinformatics

Answer 1

Correct answer is (c) Provide more permissive matching by allowing more flexible matching of residues of similar biochemical properties

To explain I would say: In this type of matching, there has to be a strict match of sequence patterns. This way of searching has a good chance of missing truly relevant motifs that have slight variations, thus generating false-negative results. As new sequences of motif are being accumulated, the rigid regular expression tends to become obsolete if not updated regularly to reflect the changes.