On the Sound Covering Cycle Problem in Paired de Bruijn Graphs

Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9130)

Abstract

Paired de Bruijn graphs are a variant of classic de Bruijn graphs used in genome assembly. In these graphs, each vertex \(v\) is associated with two labels \(\mathcal{L}(v)\) and \(\mathcal{R}(v)\). We study the NP-hard Sound Covering Cycle problem which has as input a paired de Bruijn graph \(G\) and two integers \(d\) and \(\ell \), and the task is to find a length-\(\ell \) cycle \(C\) containing all arcs of \(G\) such that for every vertex \(v\) in \(C\) and the vertex \(u\) which occurs exactly \(d\) positions after \(v\) in \(C\), we have \(\mathcal{R}(v)=\mathcal{L}(u)\). We present the first exact algorithms for this problem and several variants.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.Institut für Softwaretechnik und Theoretische InformatikTU BerlinBerlinGermany
  2. 2.LINA - UMR CNRS 6241Université de NantesSaint-NazaireFrance

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