Introduction

Identifying conserved patterns in DNA sequences, namely, motif discovery, is an important and challenging computational task. With hundreds or more sequences contained, the high-throughput sequencing data set is helpful to improve the identification accuracy of motif discovery but requires an even higher computing performance. To efficiently identify motifs in large DNA data sets, a new algorithm called PairMotifChIP is proposed by extracting and combining pairs of l-mers in the input with relatively small Hamming distance. In particular, a method for rapidly extracting pairs of l-mers is designed, which can be used not only for PairMotifChIP, but also for other DNA data mining tasks with the same demand. Experimental results on the simulated data show that the proposed algorithm can find motifs successfully and runs faster than the state-of-the-art motif discovery algorithms. Furthermore, the validity of the proposed algorithm has been verified on real data.

Publications

  1. PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets.
    Cite this
    Yu Q, Huo H, Feng D, 2016-01-01 - BioMed Research International

Credits

  1. Qiang Yu
    Developer

    School of Computer Science and Technology, Xidian University, China

  2. Hongwei Huo
    Developer

    School of Computer Science and Technology, Xidian University, China

  3. Dazheng Feng
    Investigator

    School of Electronic Engineering, Xidian University, China

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Summary
AccessionBT005269
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++
User InterfaceTerminal Command Line
Download Count0
Country/RegionChina
Submitted ByDazheng Feng