MCAST: scanning for cis-regulatory motif clusters.

ABSTRACT:

Unlabelled

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 backgr

SUBMITTER: Grant CE 

PROVIDER: S-EPMC4907379 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature