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The String Barcoding Problem is NP-Hard

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Book cover Comparative Genomics (RCG 2005)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3678))

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Abstract

The String Barcoding (SBC) problem, introduced by Rash and Gusfield (RECOMB, 2002), consists in finding a minimum set of substrings that can be used to distinguish between all members of a set of given strings. In a computational biology context, the given strings represent a set of known viruses, while the substrings can be used as probes for an hybridization experiment via microarray. Eventually, one aims at the classification of new strings (unknown viruses) through the result of the hybridization experiment. Rash and Gusfield utilized an Integer Programming approach for the solution of SBC, but they left the computational complexity of the problem as an open question. In this paper we settle the question and prove that SBC is NP-hard.

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References

  1. Cormen, T.H., Leiserson, C.E., Rivest, R.L.: Introduction to Algorithms. MIT Press, Cambridge (2001)

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  2. Garey, M.R., Johnson, D.S.: Computers and Intractability: A Guide to the Theory of NP-Completeness. W. H. Freeman and Co, New York (1979)

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  3. Karp, R.M.: Reducibility among combinatorial problems. Complexity and Computer Computations (1972)

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  4. Rash, S., Gusfield, D.: String Barcoding: Uncovering Optimal Virus Signatures. In: Proceedings of the Annual International Conference on Computational Molecular Biology (RECOMB). ACM Press, New York (2002)

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Author information

Authors and Affiliations

  1. Dipartimento di Ingegneria dell’Informazione, University of Padova,  

    Marcello Dalpasso

  2. Dipartimento di Matematica ed Informatica, University of Udine,  

    Giuseppe Lancia

  3. Dipartimento di Informatica e Telecomunicazioni, University of Trento,  

    Romeo Rizzi

Authors
  1. Marcello Dalpasso
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  2. Giuseppe Lancia
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  3. Romeo Rizzi
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Editor information

Editors and Affiliations

  1. University of Dublin, Smurfit Institute of Genetics, Trinity College, Ireland

    Aoife McLysaght

  2. Center for Bioinformatics ZBIT, Tübingen University, Sand 14, 72076, Tübingen, Germany

    Daniel H. Huson

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© 2005 Springer-Verlag Berlin Heidelberg

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Cite this paper

Dalpasso, M., Lancia, G., Rizzi, R. (2005). The String Barcoding Problem is NP-Hard. In: McLysaght, A., Huson, D.H. (eds) Comparative Genomics. RCG 2005. Lecture Notes in Computer Science(), vol 3678. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11554714_8

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  • DOI: https://doi.org/10.1007/11554714_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-28932-6

  • Online ISBN: 978-3-540-31814-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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