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Circular Sequence Comparison with q-grams

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Algorithms in Bioinformatics (WABI 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9289))

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Abstract

Sequence comparison is a fundamental step in many important tasks in bioinformatics. Traditional algorithms for measuring approximation in sequence comparison are based on the notions of distance or similarity, and are generally computed through sequence alignment techniques. As circular genome structure is a common phenomenon in nature, a caveat of specialized alignment techniques for circular sequence comparison is that they are computationally expensive, requiring from super-quadratic to cubic time in the length of the sequences. In this paper, we introduce a new distance measure based on q-grams, and show how it can be computed efficiently for circular sequence comparison. Experimental results, using real and synthetic data, demonstrate orders-of-magnitude superiority of our approach in terms of efficiency, while maintaining an accuracy very competitive to the state of the art.

R. Mercaş—Supported by the P.R.I.M.E. programme of DAAD co-funded by BMBF and EU’s 7th Framework Programme (grant 605728).

S.P. Pissis—Supported by a Research Grant (#RG130720) awarded by the Royal Society.

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Authors and Affiliations

  1. Department of Computer Science, University of Pisa and Erable Team, INRIA, Pisa, Italy

    Roberto Grossi & Nadia Pisanti

  2. Department of Informatics, King’s College London, London, UK

    Costas S. Iliopoulos, Robert Mercaş, Solon P. Pissis, Ahmad Retha & Fatima Vayani

  3. Department of Computer Science, Kiel University, Kiel, Germany

    Robert Mercaş

Authors
  1. Roberto Grossi
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  2. Costas S. Iliopoulos
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  3. Robert Mercaş
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  4. Nadia Pisanti
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  5. Solon P. Pissis
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  6. Ahmad Retha
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  7. Fatima Vayani
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Corresponding author

Correspondence to Solon P. Pissis .

Editor information

Editors and Affiliations

  1. University of Maryland, College Park, Maryland, USA

    Mihai Pop

  2. University of Lille, Lille, France

    Hélène Touzet

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Grossi, R. et al. (2015). Circular Sequence Comparison with q-grams. In: Pop, M., Touzet, H. (eds) Algorithms in Bioinformatics. WABI 2015. Lecture Notes in Computer Science(), vol 9289. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-48221-6_15

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  • DOI: https://doi.org/10.1007/978-3-662-48221-6_15

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