Title: Application of the Burrows-Wheeler Transform for searching for tandem repeats in DNA sequences

Authors: Rafal Pokrzywa

Addresses: Department of Computer Science, Silesian University of Technology, ul. Akademicka 16, 44-100 Gliwice, Poland

Abstract: Genomic sequences contain a variety of repeated structures of various lengths and types, interspersed or in tandem. Repetitive structures play an important role in molecular biology; they are related to the genetic backgrounds of inherited diseases, and they can also serve as markers for DNA mapping and DNA fingerprinting. Since biological databases keep growing in size and number there is a need for creating new tools for finding repeats in genomic sequences. This paper presents a new method for searching for tandem repeats in DNA sequences. It is based on the Burrows-Wheeler Transform (BWT), a very fast and effective data compression algorithm.

Keywords: BWT; Burrows-Wheeler transform; block sorting; tandem repeats; DNA sequences; suffix array; genomic sequences; bioinformatics; repetitive structures; data compression; genome.

DOI: 10.1504/IJBRA.2009.027517

International Journal of Bioinformatics Research and Applications, 2009 Vol.5 No.4, pp.432 - 446

Received: 26 Oct 2007
Accepted: 11 Jun 2008
Published online: 28 Jul 2009 *

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