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Approximations and Partial Solutions for the Consensus Sequence Problem

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String Processing and Information Retrieval (SPIRE 2011)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7024))

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Abstract

The problem of finding the consensus of a given set of strings is formally defined as follows: given a set of strings S = {s 1,…s k }, and a constant d, find, if it exists, a string s *, such that the Hamming distance of s * from each of the strings does not exceed d.

In this paper we study an LP relaxation for the problem. We prove an additive upper bound, depending only in the number of strings k, and randomized bounds. We show that empirical results are much better. We also compare our program with some algorithms reported in the literature, and it is shown to perform well.

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Author information

Authors and Affiliations

  1. Department of Computer Science, Bar Ilan University, Ramat Gan, 52900, Israel

    Amihood Amir, Haim Paryenty & Liam Roditty

  2. Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA

    Amihood Amir

Authors
  1. Amihood Amir
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  2. Haim Paryenty
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  3. Liam Roditty
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Editor information

Editors and Affiliations

  1. Università di Pisa, Italy

    Roberto Grossi

  2. Consiglio Nazionale delle Ricerche, Area della Ricerca di Pisa, Istituto di Scienza e Tecnologia dell’Informazione “Alessandro Faedo”, Via Giuseppe Moruzzi 1, 56124, Pisa, Italy

    Fabrizio Sebastiani  & Fabrizio Silvestri  & 

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Amir, A., Paryenty, H., Roditty, L. (2011). Approximations and Partial Solutions for the Consensus Sequence Problem. In: Grossi, R., Sebastiani, F., Silvestri, F. (eds) String Processing and Information Retrieval. SPIRE 2011. Lecture Notes in Computer Science, vol 7024. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-24583-1_17

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  • DOI: https://doi.org/10.1007/978-3-642-24583-1_17

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-24582-4

  • Online ISBN: 978-3-642-24583-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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