Exact Algorithms for Planted Motif Problems

Abstract

The problem of identifying meaningful patterns (i.e., motifs) from biological data has been studied extensively due to its paramount importance. Three versions of this problem have been identified in the literature. One of these three problems is theSeveral instances of this problem have been posed as a challenge. Numerous algorithms have been proposed in the literature that address this challenge. Many of these algorithms fall under the category of heuristic algorithms. In this paper we present algorithms for the planted (l, d)-motif problem that always find the correct answer(s). Our algorithms are very simple and are based on some ideas that are fundamentally different from the ones employed in the literature. We believe that the techniques we introduce in this paper will find independent applications.

Load Balancing for Parallel Motif Discoveries

“…While past research works have focused on improving the algorithms [4], [5], [6], [7], [8], [9], [10], and on designing hardware accelerators [11], [12], [13], [14], [15], for motif discovery, none of them focused on the load balancing issues between the master and the worker processes in the parallel execution. To the best of our knowledge this is the first paper that explored and evaluated all parameters of the parallel motif discovery problem to find the right balance for workload distributions.…”

An efficient multicore implementation of planted motif problem

“…A number of these algorithms find the approximate motif [1], [3], [4] and others find the exact motif [5], [6], [7], [8], [9], [10], [11], [12], [13], [14]. In this paper, we focus on the exact motif finding problem.…”

“…Incremental support: To address the memory issue and further enhance the runtime performance, we propose a parallel incremental approach, which is based on the incremental approach suggested in the context of sequential implementation by [9]. To solve ( , ) instance, the incremental approach works by solving the ( ′ , ) instance, where ′ ≤ , and then extending it to ( , ).…”

“…As finding candidate motif is the most expensive operation, this enhances the overall running time. The serial version of this approach is discussed in [9].…”

Subtle Motif Discovery for Detection of Dna Regulatory Sites

“…There has been a flurry of activity around this problem of subtle motifs 5,7,8 . See also 13 for some practical implementations of exact approaches. Overview of our approach.…”