PMS5: an efficient exact algorithm for the (ℓ, d)-motif finding problem.

Hieu Dinh,Sanguthevar Rajasekaran,Vamsi K Kundeti

doi:10.1186/1471-2105-12-410

Hieu Dinh, Sanguthevar Rajasekaran + Show 1 more

Open Access

https://doi.org/10.1186/1471-2105-12-410

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Journal: BMC bioinformatics	Publication Date: Oct 24, 2011
Citations: 76	License type: cc-by

Affiliation: University of Connecticut

Abstract

BackgroundMotifs are patterns found in biological sequences that are vital for understanding gene function, human disease, drug design, etc. They are helpful in finding transcriptional regulatory elements, transcription factor binding sites, and so on. As a result, the problem of identifying motifs is very crucial in biology.ResultsMany facets of the motif search problem have been identified in the literature. One of them is (ℓ, d)-motif search (or Planted Motif Search (PMS)). The PMS problem has been well investigated and shown to be NP-hard. Any algorithm for PMS that always finds all the (ℓ, d)-motifs on a given input set is called an exact algorithm. In this paper we focus on exact algorithms only. All the known exact algorithms for PMS take exponential time in some of the underlying parameters in the worst case scenario. But it does not mean that we cannot design exact algorithms for solving practical instances within a reasonable amount of time. In this paper, we propose a fast algorithm that can solve the well-known challenging instances of PMS: (21, 8) and (23, 9). No prior exact algorithm could solve these instances. In particular, our proposed algorithm takes about 10 hours on the challenging instance (21, 8) and about 54 hours on the challenging instance (23, 9). The algorithm has been run on a single 2.4GHz PC with 3GB RAM. The implementation of PMS5 is freely available on the web at http://www.pms.engr.uconn.edu/downloads/PMS5.zip.ConclusionsWe present an efficient algorithm PMS5 that uses some novel ideas and combines them with well-known algorithm PMS1 and PMSPrune. PMS5 can tackle the large challenging instances (21, 8) and (23, 9). Therefore, we hope that PMS5 will help biologists discover longer motifs in the futures.

Highlights

Motifs are patterns found in biological sequences that are vital for understanding gene function, human disease, drug design, etc
We compare the performance of PMS5 with that of other well-known exact algorithms such as Pampa [10], PMSPrune [22], Voting [20], and RISSOTO [21]
Algorithms for planted motif search are typically tested on random input datasets

Summary

Introduction

Motifs are patterns found in biological sequences that are vital for understanding gene function, human disease, drug design, etc. They are helpful in finding transcriptional regulatory elements, transcription factor binding sites, and so on. Patterns have proven to be extremely helpful in domain identification, location of protease cleavage sites, identification of signal peptides, protein interactions, determination of protein degradation elements, identification of protein trafficking elements, discovery of short functional motifs, etc. Motifs are patterns found in biological sequences that are vital for understanding many biological subjects like gene function, human disease, drug design etc. We will focus on the PMS problem (or PMS for short)

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Conclusion