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

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W201-5. doi: 10.1093/nar/gkm343. Epub 2007 May 25.


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 The MADAP web server can be accessed at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Chromatin Immunoprecipitation
  • Cluster Analysis
  • Computational Biology / methods*
  • Databases, Genetic* / statistics & numerical data
  • Genome
  • Humans
  • Internet
  • Models, Statistical
  • Open Reading Frames
  • Promoter Regions, Genetic
  • Software*