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PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets

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 h...

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Detalles Bibliográficos
Autores principales: Yu, Qiang, Huo, Hongwei, Feng, Dazheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5098105/
https://www.ncbi.nlm.nih.gov/pubmed/27843946
http://dx.doi.org/10.1155/2016/4986707
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author Yu, Qiang
Huo, Hongwei
Feng, Dazheng
author_facet Yu, Qiang
Huo, Hongwei
Feng, Dazheng
author_sort Yu, Qiang
collection PubMed
description 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.
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spelling pubmed-50981052016-11-14 PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets Yu, Qiang Huo, Hongwei Feng, Dazheng Biomed Res Int Research Article 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. Hindawi Publishing Corporation 2016 2016-10-24 /pmc/articles/PMC5098105/ /pubmed/27843946 http://dx.doi.org/10.1155/2016/4986707 Text en Copyright © 2016 Qiang Yu et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Yu, Qiang
Huo, Hongwei
Feng, Dazheng
PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets
title PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets
title_full PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets
title_fullStr PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets
title_full_unstemmed PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets
title_short PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets
title_sort pairmotifchip: a fast algorithm for discovery of patterns conserved in large chip-seq data sets
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5098105/
https://www.ncbi.nlm.nih.gov/pubmed/27843946
http://dx.doi.org/10.1155/2016/4986707
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