A new exhaustive method and strategy for finding motifs in ChIP-enriched regions.

ChIP-seq, which combines chromatin immunoprecipitation (ChIP) with next-generation parallel sequencing, allows for the genome-wide identification of protein-DNA interactions. This technology poses new challenges for the development of novel motif-finding algorithms and methods for determining exact...

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Autores principales:	Caiyan Jia, Matthew B Carson, Yang Wang, Youfang Lin, Hui Lu
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d118fcccccfa4765a9b9629de0d7da9c
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spelling	oai:doaj.org-article:d118fcccccfa4765a9b9629de0d7da9c2021-11-18T08:35:55ZA new exhaustive method and strategy for finding motifs in ChIP-enriched regions.1932-620310.1371/journal.pone.0086044https://doaj.org/article/d118fcccccfa4765a9b9629de0d7da9c2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24475069/?tool=EBIhttps://doaj.org/toc/1932-6203ChIP-seq, which combines chromatin immunoprecipitation (ChIP) with next-generation parallel sequencing, allows for the genome-wide identification of protein-DNA interactions. This technology poses new challenges for the development of novel motif-finding algorithms and methods for determining exact protein-DNA binding sites from ChIP-enriched sequencing data. State-of-the-art heuristic, exhaustive search algorithms have limited application for the identification of short (l, d) motifs (l ≤ 10, d ≤ 2) contained in ChIP-enriched regions. In this work we have developed a more powerful exhaustive method (FMotif) for finding long (l, d) motifs in DNA sequences. In conjunction with our method, we have adopted a simple ChIP-enriched sampling strategy for finding these motifs in large-scale ChIP-enriched regions. Empirical studies on synthetic samples and applications using several ChIP data sets including 16 TF (transcription factor) ChIP-seq data sets and five TF ChIP-exo data sets have demonstrated that our proposed method is capable of finding these motifs with high efficiency and accuracy. The source code for FMotif is available at http://211.71.76.45/FMotif/.Caiyan JiaMatthew B CarsonYang WangYoufang LinHui LuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 1, p e86044 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Caiyan Jia Matthew B Carson Yang Wang Youfang Lin Hui Lu A new exhaustive method and strategy for finding motifs in ChIP-enriched regions.
description	ChIP-seq, which combines chromatin immunoprecipitation (ChIP) with next-generation parallel sequencing, allows for the genome-wide identification of protein-DNA interactions. This technology poses new challenges for the development of novel motif-finding algorithms and methods for determining exact protein-DNA binding sites from ChIP-enriched sequencing data. State-of-the-art heuristic, exhaustive search algorithms have limited application for the identification of short (l, d) motifs (l ≤ 10, d ≤ 2) contained in ChIP-enriched regions. In this work we have developed a more powerful exhaustive method (FMotif) for finding long (l, d) motifs in DNA sequences. In conjunction with our method, we have adopted a simple ChIP-enriched sampling strategy for finding these motifs in large-scale ChIP-enriched regions. Empirical studies on synthetic samples and applications using several ChIP data sets including 16 TF (transcription factor) ChIP-seq data sets and five TF ChIP-exo data sets have demonstrated that our proposed method is capable of finding these motifs with high efficiency and accuracy. The source code for FMotif is available at http://211.71.76.45/FMotif/.
format	article
author	Caiyan Jia Matthew B Carson Yang Wang Youfang Lin Hui Lu
author_facet	Caiyan Jia Matthew B Carson Yang Wang Youfang Lin Hui Lu
author_sort	Caiyan Jia
title	A new exhaustive method and strategy for finding motifs in ChIP-enriched regions.
title_short	A new exhaustive method and strategy for finding motifs in ChIP-enriched regions.
title_full	A new exhaustive method and strategy for finding motifs in ChIP-enriched regions.
title_fullStr	A new exhaustive method and strategy for finding motifs in ChIP-enriched regions.
title_full_unstemmed	A new exhaustive method and strategy for finding motifs in ChIP-enriched regions.
title_sort	new exhaustive method and strategy for finding motifs in chip-enriched regions.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/d118fcccccfa4765a9b9629de0d7da9c
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A new exhaustive method and strategy for finding motifs in ChIP-enriched regions.

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