Application of the Burrows-Wheeler Transform for searching for tandem repeats in DNA sequences.
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.
Pokrzywa
Rafal
R
Department of Computer Science, Silesian University of Technology, ul. Akademicka 16, 44-100 Gliwice, Poland. rafal.pokrzywa@gmail.com
D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry; D016172:DNA Fingerprinting; D044962:Data Compression / Q000379:methods; D016678:Genome; D010363:Pattern Recognition, Automated / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D020080:Tandem Repeat Sequences
D004247:DNA