Nucleic Acids Research, 2001, Vol. 29, No. 22 4633-4642
© 2001 Oxford University Press
REPuter: the manifold applications of repeat analysis on a genomic scale
Faculty of Technology, University of Bielefeld, PO Box 10 01 31, D-33501 Bielefeld, Germany, 1Artemis Pharmaceuticals, Neurather Ring 1, 51063 Köln, Germany and 2Max Planck Institute for Molecular Genetics, Department for Computational Molecular Biology, Ihnestrasse 73, 14195 Berlin, Germany
The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter program described herein was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance and interactive visualization. This article circumscribes the wide scope of repeat analysis using applications in five different areas of sequence analysis: checking fragment assemblies, searching for low copy repeats, finding unique sequences, comparing gene structures and mapping of cDNA/EST sequences.
* To whom correspondence should be addressed. Tel: +49 521 106 2906; Fax: +49 521 106 6411; Email: kurtz{at}techfak.uni-bielefeld.de
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