On NP-Hardness of the Paired de Bruijn Sound Cycle Problem

  • Evgeny Kapun
  • Fedor Tsarev
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8126)

Abstract

The paired de Bruijn graph is an extension of de Bruijn graph incorporating mate pair information for genome assembly proposed by Mevdedev et al. However, unlike in an ordinary de Bruijn graph, not every path or cycle in a paired de Bruijn graph will spell a string, because there is an additional soundness constraint on the path. In this paper we show that the problem of checking if there is a sound cycle in a paired de Bruijn graph is NP-hard in general case. We also explore some of its special cases, as well as a modified version where the cycle must also pass through every edge.

Keywords

paired de Bruijn graph genome assembly complexity NP-hard 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Evgeny Kapun
    • 1
  • Fedor Tsarev
    • 1
  1. 1.Mechanics and Optics Genome Assembly Algorithms LaboratorySt. Petersburg National Research University of Information TechnologiesSt. PetersburgRussia

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