An Affinity Propagation-Based DNA Motif Discovery Algorithm

BioMed Research International
Chunxiao SunZhigang Sun

Abstract

The planted (l, d) motif search (PMS) is one of the fundamental problems in bioinformatics, which plays an important role in locating transcription factor binding sites (TFBSs) in DNA sequences. Nowadays, identifying weak motifs and reducing the effect of local optimum are still important but challenging tasks for motif discovery. To solve the tasks, we propose a new algorithm, APMotif, which first applies the Affinity Propagation (AP) clustering in DNA sequences to produce informative and good candidate motifs and then employs Expectation Maximization (EM) refinement to obtain the optimal motifs from the candidate motifs. Experimental results both on simulated data sets and real biological data sets show that APMotif usually outperforms four other widely used algorithms in terms of high prediction accuracy.

References

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Citations

Sep 14, 2016·Computational Biology and Chemistry·Abdolvahed PariSaeed Parseh
Nov 25, 2016·BioMed Research International·Yipu ZhangMaode Yan
Aug 16, 2019·Entropy·Chun-Xiao SunWen-Hu Wang

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Methods Mentioned

BETA
ChIP-Seq

Software Mentioned

Weblogo
AlignACE
VINE
PairMotif
MCEMDA
CRMD
RISOTTO
APMotif
MEME

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