Discovering cis-Regulatory Motifs

UMMS Affiliation

Program in Bioinformatics and Integrative Biology; Department of Biochemistry and Molecular Pharmacology

Publication Date


Document Type



Bioinformatics | Computational Biology


This protocol describes a suite of tools for motif finding, using cis-regulatory motifs as an example. The first part of this protocol demonstrates the use of MEME (ab initio motif discovery), JASPAR (a motif database), Clover (searching for enriched known motifs), and MAST (scanning a sequence for motif sites) on a set of computationally predicted CREB-binding sequences downloaded from the UCSC Table Browser. The second part of the protocol shows how to use MEME-ChIP, an integrated suite of tools for analyzing ChIP-seq data, to discover motifs in STAT1 ChIP-seq peaks and compare them with known motifs in the JASPAR database.

DOI of Published Version



Cold Spring Harb Protoc. 2017 Feb 1;2017(2):pdb.prot093203. doi: 10.1101/pdb.prot093203. Link to article on publisher's site

Journal/Book/Conference Title

Cold Spring Harbor protocols

Related Resources

Link to Article in PubMed

PubMed ID