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Research on Algorithms for Planted (l,d) Motif Search

Conference paper
Part of the Communications in Computer and Information Science book series (CCIS, volume 950)

Abstract

As one of the most challenging problems in bioinformatics, motif search has important implications for gene discovery and understanding of gene regulatory relationships. Planted (l,d) motif searching (PMS) is a widely accepted issue model in the field of motif search. Solving PMS issues involve computer science, bioinformatics and other related knowledge. Of course, a huge amount of computation is probably unavoidable. Designing an effective and optimized method is particularly important for solving the puzzle.

This article mainly introduces and implements related algorithms for planted (l,d) motif search. Firstly, according to the different implementation methods, it can be divided into two categories: enumeration algorithm and local search algorithm. Then four algorithms are proposed to solve the issue, pseudocodes are also available. Finally, in the experimental part, PMSP algorithm has the best performance through programing implementation and operating results evaluation. In the following work, by combining the idea of MapReduce parallel computing, the design of PMSPMR algorithm can achieve more excellent operational results.

Keywords

Planted (l,d) motif search Execution time MapReduce 

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Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  1. 1.School of Computer ScienceXi’an Shiyou UniversityXi’anChina

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