A New Exhaustive Method and Strategy for Finding Motifs in ChIP-Enriched Regions

作者：Jia, Caiyan^*; Carson, Matthew B.; Wang, Yang; Lin, Youfang; Lu, Hui

来源：PLos One, 2014, 9(1): e86044.

DOI：10.1371/journal.pone.0086044

• FACTOR-BINDING SITES
• SEQ DATA
• TRANSCRIPTION
• DISCOVERY
• DNA
• GENOME
• IDENTIFICATION
• ALGORITHMS
• SEQUENCES
• DATABASE

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/.

• 出版日期2014-1-24
• 单位北京交通大学; 河北医科大学; 西北大学; 上海交通大学