RT Journal Article
SR Electronic
T1 iFORM: incorporating Find Occurrence of Regulatory Motifs
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 044214
DO 10.1101/044214
A1 Chao Ren
A1 Hebing Chen
A1 Feng Liu
A1 Hao Li
A1 Xiaochen Bo
A1 Wenjie Shu
YR 2016
UL http://biorxiv.org/content/early/2016/03/16/044214.abstract
AB Motivation Accurately identifying binding sites of transcription factors (TFs) is crucial to understand the mechanisms of transcriptional regulation and human disease.Results We present incorporating Find Occurrence of Regulatory Motifs (iFORM), an easy-to-use tool for scanning DNA sequence with TF motifs described as position weight matrices (PWMs). iFORM achieves higher accuracy and sensitivity by integrating the results from five classical motif discovery programs based on Fisher’s combined probability test. We have used iFORM to provide accurate results on a variety of data in the ENCODE Project and the NIH Roadmap Epigenomics Project, and has demonstrated its utility to further understand individual roles of functional elements.Availability iFORM can be freely accessed athttps://github.com/wenjiegroup/iFORM.Contact shuwj{at}bmi.ac.cn and boxc{at}bmi.ac.cn