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Nucleic Acids Research Advance Access first published online on May 25, 2007
This version published online on June 8, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm343
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data

Christoph D. Schmid1,*, Thierry Sengstag1,2, Philipp Bucher1,3 and Mauro Delorenzi1,2

1Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland 2National Centre of Competence in Research (NCCR) Molecular Oncology, Swiss Institute of Experimental Cancer Research (ISREC), Epalinges, Switzerland and 3Swiss Institute of Experimental Cancer Research (ISREC), Epalinges, Switzerland

*To whom correspondence should be addressed. Tel: +41 21 692 59 56; Fax: +41 21 692 59 45; Email: christoph.schmid{at}isb-sib.ch

Received January 31, 2007. Revised April 5, 2007. Accepted April 22, 2007.

A recurring task in the analysis of mass genome annotation data from high-throughput technologies is the identification of peaks or clusters in a noisy signal profile. Examples of such applications are the definition of promoters on the basis of transcription start site profiles, the mapping of transcription factor binding sites based on ChIP-chip data and the identification of quantitative trait loci (QTL) from whole genome SNP profiles. Input to such an analysis is a set of genome coordinates associated with counts or intensities. The output consists of a discrete number of peaks with respective volumes, extensions and center positions. We have developed for this purpose a flexible one-dimensional clustering tool, called MADAP, which we make available as a web server and as standalone program. A set of parameters enables the user to customize the procedure to a specific problem. The web server, which returns results in textual and graphical form, is useful for small to medium-scale applications, as well as for evaluation and parameter tuning in view of large-scale applications, requiring a local installation. The program written in C++ can be freely downloaded from ftp://ftp.epd.unil.ch/pub/software/unix/madap. The MADAP web server can be accessed at http://www.isrec.isb-sib.ch/madap/.

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