Exact algorithms for motif search
نویسندگان
چکیده
In this paper we study the problem of identifying meaningful patterns (i.e., motifs) from biological data. The general version of this problem is NP-hard. Numerous algorithms have been proposed in the literature to solve this problem. Many of these algorithms fall under the category of approximation algorithms. We concentrate on exact algorithms in this paper. In particular, we concentrate on two different versions of the motif search problem and offer exact algorithms for two of them. The proposed algorithms perform better than some of the bestknown algorithms. * This research was supported in part by the NSF Grants CCR-9912395 and ITR0326155.
منابع مشابه
Space and Time Efficient Algorithms for Planted Motif Search
We consider the (l, d) Planted Motif Search Problem, a problem that arises from the need to find transcription factor-binding sites in genomic information. We propose the algorithms PMSi and PMSP which are based on ideas considered in PMS1 [6]. These algorithms are exact, make use of less space than the known exact algorithms such as PMS and are able to tackle instances with large values of d. ...
متن کاملDevelopment of an Efficient Hybrid Method for Motif Discovery in DNA Sequences
This work presents a hybrid method for motif discovery in DNA sequences. The proposed method called SPSO-Lk, borrows the concept of Chebyshev polynomials and uses the stochastic local search to improve the performance of the basic PSO algorithm as a motif finder. The Chebyshev polynomial concept encourages us to use a linear combination of previously discovered velocities beyond that proposed b...
متن کاملPairMotif: A New Pattern-Driven Algorithm for Planted (l, d) DNA Motif Search
Motif search is a fundamental problem in bioinformatics with an important application in locating transcription factor binding sites (TFBSs) in DNA sequences. The exact algorithms can report all (l, d) motifs and find the best one under a specific objective function. However, it is still a challenging task to identify weak motifs, since either a large amount of memory or execution time is requi...
متن کاملComparison of particle swarm optimization and tabu search algorithms for portfolio selection problem
Using Metaheuristics models and Evolutionary Algorithms for solving portfolio problem has been considered in recent years.In this study, by using particles swarm optimization and tabu search algorithms we optimized two-sided risk measures . A standard exact penalty function transforms the considered portfolio selection problem into an equivalent unconstrained minimization problem. And in final...
متن کاملAn Efficient Motif Search Algorithm Based on a Minimal Forbidden Patterns Approach
One of the problems arising in the analysis of biological sequences is the discovery of sequence similarity by finding common motifs. Several versions of the motif finding problem have been proposed for dealing with this problem and for each version, numerous algorithms have been developed. In this paper, we propose an exact algorithm, called SMS-H-FORBID to solve the Simple Motif Problem (SMP)...
متن کامل