Extending Pattern Branching to Handle Challenging Instances

We consider the planted motif search problem, a problem that arises from the need to find transcription factor-binding sites in genomic information. One of the fastest non-exact algorithms that solves this problem is Pattern Branching [10], however this algorithm fails to solve challenging instances such as (15, 5) in most cases. In this paper we discuss a simple extension to this algorithm and an implementation of it that allows us to tackle challenging instances such as (15, 5) and (17, 6) with accuracy close to 100%.

• Type: Conference
• Year: 2006
• Where: BIBE
• Authors: Jaime Davila, Sanguthevar Rajasekaran
• Keywords: BIBE 2006, Bioinformatics, Challenging Instances, Fastest Non-exact Algorithms, Motif Search Problem