Publication Date:
2016-04-08
Description:
: 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 http://meme-suite.org and http://alternate.meme-suite.org . Contact: t.bailey@imb.uq.edu.au or william-noble@uw.edu Supplementary information : Supplementary data are available at Bioinformatics online.
Print ISSN:
1367-4803
Electronic ISSN:
1460-2059
Topics:
Biology
,
Computer Science
,
Medicine
