Efficient Sequential and Parallel Algorithms for Planted Motif Search

TL;DR

This paper introduces PMS8, an exact parallel algorithm for Planted Motif Search that efficiently solves challenging instances and larger parameters, advancing the computational methods for biological motif detection.

Contribution

The paper presents PMS8, the first parallel algorithm capable of solving difficult (l,d) instances and larger parameters for PMS, with new conditions for common d-neighbors among l-mers.

Findings

PMS8 solves (25,10) and (26,11) instances.

PMS8 is efficient on larger instances like (50,21).

Introduces conditions for 3 l-mers to share a common d-neighbor.

Abstract

Motif searching is an important step in the detection of rare events occurring in a set of DNA or protein sequences. One formulation of the problem is known as (l,d)-motif search or Planted Motif Search (PMS). In PMS we are given two integers l and d and n biological sequences. We want to find all sequences of length l that appear in each of the input sequences with at most d mismatches. The PMS problem is NP-complete. PMS algorithms are typically evaluated on certain instances considered challenging. This paper presents an exact parallel PMS algorithm called PMS8. PMS8 is the first algorithm to solve the challenging (l,d) instances (25,10) and (26,11). PMS8 is also efficient on instances with larger l and d such as (50,21). This paper also introduces necessary and sufficient conditions for 3 l-mers to have a common d-neighbor.