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...

Full description

Bibliographic Details
Main Authors: Caiyan Jia, Matthew B Carson, Yang Wang, Youfang Lin, Hui Lu
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2014-01-01
Series:PLoS ONE
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24475069/?tool=EBI
id doaj-d118fcccccfa4765a9b9629de0d7da9c
record_format Article
spelling doaj-d118fcccccfa4765a9b9629de0d7da9c2021-03-03T20:16:40ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0191e8604410.1371/journal.pone.0086044A new exhaustive method and strategy for finding motifs in ChIP-enriched regions.Caiyan JiaMatthew B CarsonYang WangYoufang LinHui LuChIP-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/.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24475069/?tool=EBI
collection DOAJ
language English
format Article
sources DOAJ
author Caiyan Jia
Matthew B Carson
Yang Wang
Youfang Lin
Hui Lu
spellingShingle Caiyan Jia
Matthew B Carson
Yang Wang
Youfang Lin
Hui Lu
A new exhaustive method and strategy for finding motifs in ChIP-enriched regions.
PLoS ONE
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)
series PLoS ONE
issn 1932-6203
publishDate 2014-01-01
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/.
url https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24475069/?tool=EBI
work_keys_str_mv AT caiyanjia anewexhaustivemethodandstrategyforfindingmotifsinchipenrichedregions
AT matthewbcarson anewexhaustivemethodandstrategyforfindingmotifsinchipenrichedregions
AT yangwang anewexhaustivemethodandstrategyforfindingmotifsinchipenrichedregions
AT youfanglin anewexhaustivemethodandstrategyforfindingmotifsinchipenrichedregions
AT huilu anewexhaustivemethodandstrategyforfindingmotifsinchipenrichedregions
AT caiyanjia newexhaustivemethodandstrategyforfindingmotifsinchipenrichedregions
AT matthewbcarson newexhaustivemethodandstrategyforfindingmotifsinchipenrichedregions
AT yangwang newexhaustivemethodandstrategyforfindingmotifsinchipenrichedregions
AT youfanglin newexhaustivemethodandstrategyforfindingmotifsinchipenrichedregions
AT huilu newexhaustivemethodandstrategyforfindingmotifsinchipenrichedregions
_version_ 1714823153959567360