MCAST: scanning for cis-regulatory motif clusters

Grant, Charles E., Johnson, James, Bailey, Timothy L. and Noble, William Stafford (2016) MCAST: scanning for cis-regulatory motif clusters. Bioinformatics, 32 8: 1217-1219. doi:10.1093/bioinformatics/btv750

Author Grant, Charles E.
Johnson, James
Bailey, Timothy L.
Noble, William Stafford
Title MCAST: scanning for cis-regulatory motif clusters
Formatted title
MCAST: scanning for cis-regulatory motif clusters
Journal name Bioinformatics   Check publisher's open access policy
ISSN 1367-4803
Publication date 2016-04-15
Year available 2015
Sub-type Article (original research)
DOI 10.1093/bioinformatics/btv750
Open Access Status Not Open Access
Volume 32
Issue 8
Start page 1217
End page 1219
Total pages 3
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Formatted abstract
Summary: Precise regulatory control of genes, particularly in eukaryotes, frequently requires the joint action of multiple sequence-specific transcription factors. A cis-regulatory module (CRM) is a genomic locus that is responsible for gene regulation and that contains multiple transcription factor binding sites in close proximity. Given a collection of known transcription factor binding motifs, many bioinformatics methods have been proposed over the past 15 years for identifying within a genomic sequence candidate CRMs consisting of clusters of those motifs.
Results: The MCAST algorithm uses a hidden Markov model with a P-value-based scoring scheme to identify candidate CRMs. Here, we introduce a new version of MCAST that offers improved graphical output, a dynamic background model, statistical confidence estimates based on false discovery rate estimation and, most significantly, the ability to predict CRMs while taking into account epigenomic data such as DNase I sensitivity or histone modification data. We demonstrate the validity of MCAST’s statistical confidence estimates and the utility of epigenomic priors in identifying CRMs.
Availability and implementation: MCAST is part of the MEME Suite software toolkit. A web server and source code are available at and
Q-Index Code CX
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
Institute for Molecular Bioscience - Publications
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Created: Wed, 06 Apr 2016, 01:24:17 EST by Susan Allen on behalf of Institute for Molecular Bioscience