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CPmodule specifications


Unique identifier OMICS_12899
Name CPmodule
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Either you provide fasta target and background sequence and a file with PWMs, and then all 3 phases will be done; or you provide the clover files directly and then only the last 2 phases are done.
Input format .txt, .fa
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 0.6
Stability Stable
Source code URL https://dtai.cs.kuleuven.be/CP4IM/CPmodule/data/cpmodule-0.6.tar.gz
Maintained Yes




No version available


  • person_outline Siegfried Nijssen

Publication for CPmodule

CPmodule citations


A New Algorithm for Identifying Cis Regulatory Modules Based on Hidden Markov Model

Biomed Res Int
PMCID: 5405574
PMID: 28497059
DOI: 10.1155/2017/6274513

[…] is dataset, following the way of three other HMM-based methods, Cluster-Buster, Stubb, and BayCis, all sequences are used as the training set and the testing set simultaneously for ComSPS. For Stubb, CPModule, and MotEvo, which depend on window size settings, they were tested with three window size settings, 100 bp, 150 bp, and 200 bp, which are around the average length of CRMs. Other parameters […]


De novo prediction of cis regulatory elements and modules through integrative analysis of a large number of ChIP datasets

BMC Genomics
PMCID: 4265420
PMID: 25442502
DOI: 10.1186/1471-2164-15-1047

[…] ence of motifs in a large number of ChIP-seq datasets for different TFs from different cell types, tissues, developmental stages and physiological conditions. Although a few methods such as SpaMo [], CPModule [] and [], have been made to identify CREs of cooperator TFs in a ChIP-seq dataset, they do not integrate multiple ChIP-seq datasets, and cannot predict novel motifs in CRMs, as they all depe […]


Unveiling combinatorial regulation through the combination of ChIP information and in silico cis regulatory module detection

Nucleic Acids Res
PMCID: 3384348
PMID: 22422841
DOI: 10.1093/nar/gks237

[…] We first use a synthetic data set to compare CPModule with different CRM detection tools. The synthetic data is retrieved from Xie et al. (). The data consists of 22 genomic sequences each 1000 base pairs in length. In 20 sequences, sites sample […]


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CPmodule institution(s)
Department of Computer Science, Katholieke Universiteit Leuven, Belgium; Department of Microbial and Molecular systems, Katholieke Universiteit Leuven, Belgium
CPmodule funding source(s)
Project grant (SBO-BioFrame), agency for Innovation by Science and Technology in Flanders (IWT-Vlaanderen); Postdoc grant from the Research Foundation Flanders

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