Research on Algorithms for Planted (l,d) Motif Search
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.
KeywordsPlanted (l,d) motif search Execution time MapReduce
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