Discovering cis-regulatory motifs

Jui-Hung Hung, Zhiping Weng

Research output: Contribution to journalArticle

3 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)173-181
Number of pages9
JournalCold Spring Harbor Protocols
Volume2017
Issue number2
DOIs
StatePublished - 1 Feb 2017

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