Molecular Cloning Fourth Edition, A Laboratory Manual, by Michael R. Green and Joseph Sambrook

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Discovering cis-Regulatory Motifs

(Protocol summary only for purposes of this preview site)

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 (Bailey et al. 2006) (ab initio motif discovery), JASPAR (Portales-Casamar et al. 2010) (a motif database), Clover (Frith et al. 2004) (searching for enriched known motifs), and MAST (Bailey and Gribskov 1998) (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 (Machanick and Bailey 2011), 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.


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(Limited time special offer.) Molecular Cloning Fourth Edition, A Laboratory Manual, by Michael R. Green and Joseph Sambrook
Molecular Cloning Fourth Edition, A Laboratory Manual, by Michael R. Green and Joseph Sambrook

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