Computation and Visualization of Degenerate Repeats in Complete Genomes

Stefan Kurtz, Enno Ohlebusch, and Chris Schleiermacher, University of Bielefeld; Jens Stoye, German Cancer Reserch Center; and Robert Giegerich, University of Bielefeld

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 family of programs described herein was designed to serve asa fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance, interactive visualization, and simple interfacing to other analysis programs.

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