SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data.

ABSTRACT: The identification of transcription factor binding motifs is important for the study of gene transcriptional regulation. The chromatin immunoprecipitation (ChIP), followed by massive parallel sequencing (ChIP-seq) experiments, provides an unprecedented opportunity to discover binding motifs. Computational methods have been developed to identify motifs from ChIP-seq data, while at the same time encountering several problems. For example, existing methods are often not scalable to the large number of sequences obtained from ChIP-seq peak regions. Some methods heavily rely on well-annotated motifs even though the number of known motifs is limited. To simplify the problem, de novo motif discovery methods often neglect underrepresented motifs in ChIP-seq peak regions. To address these issues, w

SUBMITTER: Ding J 

PROVIDER: S-EPMC3950686 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature