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Application of the Burrows-Wheeler Transform for Searching for Approximate Tandem Repeats

  • Agnieszka Danek
  • Rafał Pokrzywa
  • Izabela Makałowska
  • Andrzej Polański
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7632)

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.

Keywords

approximate tandem repeats Burrows-Wheeler transform suffix array Hamming distance 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Agnieszka Danek
    • 1
  • Rafał Pokrzywa
    • 1
  • Izabela Makałowska
    • 2
  • Andrzej Polański
    • 1
  1. 1.Institute of InformaticsSilesian University of TechnologyGliwicePoland
  2. 2.Laboratory of Bioinformatics, Faculty of BiologyAdam Mickiewicz UniversityPoznańPoland

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