期刊名称：Journal of Theoretical and Applied Information Technology
印刷版ISSN：1992-8645
电子版ISSN：1817-3195
出版年度：2016
卷号：89
期号：2
出版社：Journal of Theoretical and Applied
摘要：The Identification of inimitable patterns (motif) occurring in a set of biological sequences could give rise to new biological discoveries and has been studied considerably due to its paramount importance. In the field of bioinformatics, motif search is the vital problem for its application in the detection of transcriptional regulatory elements and transcription factor binding sites (TFBS) which are crucial for the knowledge of drug design, human disease, gene function etc. Many aspects of the motif search problem have been identified in the literature. One of them is the planted (ℓ, d)-motif search problem. In this paper, we propose a parallel extension of the existing PMSPRUNE algorithm along with two additional features: those are neighbor generation on a demand basis and omitting the duplicate neighbor checking with the help of a bit vector implementation. The experimental result shows, the proposed multicore algorithm in C, handles the problem for larger d value with fix length ℓ with a speed up more than twice, without any additional requirement of space on a 2.4GHz PC with 4GB RAM.
