J. V. Choudhuri, E. Ohlebusch,
C. Schleiermacher, J. Stoye, and R. Giegerich:
REPuter: the Manifold Applications
of Repeat Analysis
on a Genomic Scale.
Nucleic Acids Research, 29(22):4633--4642,
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.