On the Challenging Instances of the Planted Motif Problem

A classic problem of motif discovery in DNA sequences, called the Planted (l, d)-Motif Problem has been widely studied over the past decade owing to its application in identifying vital signals such as transcription factor binding sites. Challenging instances of the problem are those that have been probabilistically proved as ‘difficult to be solved’ due to the existence of several motifs by random chance for such instances. In this work, we present an expected case analysis that helps understanding the real ‘challenging instances’ of the problem.