FisherMP: fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets.

ABSTRACT: Detecting binding motifs of combinatorial transcription factors (TFs) from chromatin immunoprecipitation sequencing (ChIP-seq) experiments is an important and challenging computational problem for understanding gene regulations. Although a number of motif-finding algorithms have been presented, most are either time consuming or have sub-optimal accuracy for processing large-scale datasets. In this article, we present a fully parallelized algorithm for detecting combinatorial motifs from ChIP-seq datasets by using Fisher combined method and OpenMP parallel design. Large scale validations on both synthetic data and 350 ChIP-seq datasets from the ENCODE database showed that FisherMP has not only super speeds on large datasets, but also has high accuracy when compared with multiple popular met

SUBMITTER: Zhang S 

PROVIDER: S-EPMC6589551 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature