PT  - JOURNAL ARTICLE
AU  - Chao Ren
AU  - Hebing Chen
AU  - Feng Liu
AU  - Hao Li
AU  - Xiaochen Bo
AU  - Wenjie Shu
TI  - iFORM: incorporating Find Occurrence of Regulatory Motifs
AID  - 10.1101/044214
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 044214
4099  - http://biorxiv.org/content/early/2016/03/16/044214.short
4100  - http://biorxiv.org/content/early/2016/03/16/044214.full
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