Application of the Burrows-Wheeler transform for searching for approximate tandem repeats

Abstract

Tandem repeats (TRs) are contiguous copies of repeating patterns, which may be either exact or approximate. Approximate tandem repeats (ATRs) in a genomic sequences are adjacent copies of a repeating pattern of nucleotides, where similarity is defined by a suitable measure. Both TRs and ATRs are used in forensic analysis, DNA mapping, testing for inherited diseases and many evolutionary studies. All their functions and roles are not well defined and remains a subject of ongoing investigation. However, growing biological databases together with tools to look for such repeats may lead to better understanding of their behavior. This paper presents our method for searching for ATRs defined on the basis of the model of substitution mutations and its comparison to two other tools. The capabilities and limitations of methods are analyzed and results obtained with each tool are investigated. © 2012 Springer-Verlag.