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CATCHprofiles | Clustering and alignment tool for ChIP profiles


A standalone for exhaustive pattern detection in ChIP profiling data. CATCHprofiles is built upon a computationally efficient implementation for the exhaustive alignment and hierarchical clustering of ChIP profiling data. The tool features a graphical interface for examination and browsing of the clustering results. CATCHprofiles requires no prior knowledge about functional sites, detects known binding patterns ‘‘ab initio’’, and enables the detection of new patterns from ChIP data at a high resolution, exemplified by the detection of asymmetric histone and histone modification patterns around H2A.Z-enriched sites. CATCHprofiles’ capability for exhaustive analysis combined with its ease-of-use makes it an invaluable tool for explorative research based on ChIP profiling data.

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CATCHprofiles classification

CATCHprofiles specifications

Unique identifier:
Software type:
Restrictions to use:
Input format:
Output format:
Programming languages:
C, Java
Clustering and AlignmenT of ChIp profiles
Graphical user interface
Input data:
Selected areas from the ChIP profiling data, e.g. areas obtained from peak calling, or areas selected from annotation, such as promoter regions
Output data:
Profile patterns, positions, cluster tree
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:

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CATCHprofiles support



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Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands; Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark; Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, Netherlands; eScience Centre, University of Copenhagen, Copenhagen, Denmark

Funding source(s)

This work was funded in part by the European HEROIC project for epigenetic research (EU FP6 Integrated Project), by the Stichting Nationale Computerfaciliteiten (National Computing Facilities Foundation, NCF), by the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organization for Scientific Research, NOW).

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