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A BLAST-Based Algorithm to Find Evenly Distributed Unique Subsequences

  • Maciej Kulawik
  • Robert M. NowakEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11089)

Abstract

Genomics rearrangements detection involves processing of large amounts of DNA data and therefore efficiency of the used algorithms is crucial. We propose the algorithm based on evenly distributed unique subsequences. In this paper BLAST-based pattern matching is examined in terms of computation time and detection quality. The experiments were carried out both on real sequence with artificially introduced random rearrangements. The algorithm extension was implemented as part of genomecmp web application which provides graphical user interface for ease and convenience of use.

Keywords

Bioinformatics Genomics rearrangements detection Computer program Marker BLAST 

References

  1. 1.
    Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. J. Mol. Biol. 215(3), 403–410 (1990).  https://doi.org/10.1016/S0022-2836(05)80360-2. http://www.sciencedirect.com/science/article/pii/S0022283605803602CrossRefGoogle Scholar
  2. 2.
    Knuth, D.E., Morris, J.H., Pratt, V.R.: Fast pattern matching in strings. SIAM J. Comput. 6(2), 323–350 (1977).  https://doi.org/10.1137/0206024MathSciNetCrossRefzbMATHGoogle Scholar
  3. 3.
    Kent, W.J.: Blatthe blast-like alignment tool. Genome Res. 12(4), 656–664 (2002)CrossRefGoogle Scholar
  4. 4.
    Kulawik, M., Nowak, R.M.: Genomecmp: computer software to detect genomic rearrangements using markers (2017).  https://doi.org/10.1117/12.2280483
  5. 5.
    Myers, E.W.: An O(ND) difference algorithm and its variations. Algorithmica 1(1–4), 251–266 (1986)MathSciNetCrossRefGoogle Scholar
  6. 6.
    Tattini, L., D’Aurizio, R., Magi, A.: Detection of genomic structural variants from next-generation sequencing data. Front. Bioeng. Biotechnol. 3, 92 (2015)CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  1. 1.Institute of Computer ScienceWarsaw University of TechnologyWarsawPoland

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