A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data

Ngoc Tam L Tran,Chun-Hsi Huang

doi:10.1186/1745-6150-9-4

Abstract

ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools facilitate the motif detection by providing user-friendly Web interface. In this work, we reviewed nine motif finding Web tools that are capable for detecting binding site motifs in ChIP-Seq data. We showed each motif finding Web tool has its own advantages for detecting motifs that other tools may not discover. We recommended the users to use multiple motif finding Web tools that implement different algorithms for obtaining significant motifs, overlapping resemble motifs, and non-overlapping motifs. Finally, we provided our suggestions for future development of motif finding Web tool that better assists researchers for finding motifs in ChIP-Seq data.ReviewersThis article was reviewed by Prof. Sandor Pongor, Dr. Yuriy Gusev, and Dr. Shyam Prabhakar (nominated by Prof. Limsoon Wong).

Highlights

The Generation Sequencing (NGS) technology has revolutionized the genetics studies of RNA-Seq for transcriptome analysis and ChIP-Seq for DNA-proteins interaction [1]
We presented that different peak calling tools implement different algorithms for targeting different types of peaks
It is critical for the users to pick a suitable peak calling tool for the type of research being conducted so that it can maximize the chance for obtaining the best possible peak sequences for finding the motifs

Summary

Introduction

The Generation Sequencing (NGS) technology has revolutionized the genetics studies of RNA-Seq for transcriptome analysis and ChIP-Seq for DNA-proteins interaction [1]. ChIP-Seq has become the method of choice for genome-wide characterization of transcription factor binding, polymerase binding, and histone modifications [2]. The identification of binding sites by transcription factors, polymerase, or histone modification marks plays a crucial role for identifying the regulatory elements that regulate the gene expression. The binding sites for TF in ChIP-Seq are usually located in close proximity of the summit points of the peaks [3]. Many tools have been developed for motif finding. Recent motif finding development provides user-friendliness via Web interface. We surveyed nine motif finding Web tools that are capable for finding motifs in ChIP-Seq data.

Results

Discussion

Conclusion