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On Algorithmic Complexity of Biomolecular Sequence Assembly Problem

  • Giuseppe Narzisi
  • Bud Mishra
  • Michael C. Schatz
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8542)

Abstract

Because of its connection to the well-known \(\mathcal{NP}\)-complete shortest superstring combinatorial optimization problem, the Sequence Assembly Problem (SAP) has been formulated in simple and sometimes unrealistic string and graph-theoretic frameworks. This paper revisits this problem by re-examining the relationship between the most common formulations of the SAP and their computational tractability under different theoretical frameworks. For each formulation we show examples of logically-consistent candidate solutions which are nevertheless unfeasible in the context of the underlying biological problem. This material is hoped to be valuable to theoreticians as they develop new formulations of SAP as well as of guidance to developers of new pipelines and algorithms for sequence assembly and variant detection.

Keywords

Genome Assembly Sequence Assembly Problem Optimality \(\mathcal{NP}\)-complete Problem 

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Giuseppe Narzisi
    • 1
  • Bud Mishra
    • 1
    • 2
  • Michael C. Schatz
    • 1
  1. 1.Cold Spring Harbor LaboratorySimons Center for Quantitative BiologyUSA
  2. 2.Courant Institute of Mathematical SciencesNew York UniversityNew YorkUSA

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