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An Efficient Algorithm for De Novo Peptide Sequencing

  • S. Brunetti
  • D. Dutta
  • S. Liberatori
  • E. Mori
  • D. Varrazzo
Conference paper

Abstract

In this paper we propose a new algorithm for the de novo peptide sequencing problem. This problem reconstructs a peptide sequence from a given tandem mass spectra data containing n peaks. We first build a directed acyclic graph G = (V, E) in O(n log n) time, where vV is a spectrum mass ion or a complementary mass to a spectrum ion. The solutions of this problem are then given by the paths in the graph between two designated vertices. Unlike previous approaches, the proposed algorithm does not use dynamic programming, but it builds the graph in a progressive fashion using a priority queue, thus obtaining an improvement over other methods [1,2].

Keywords

Directed Acyclic Graph Mass Peak Priority Queue Dynamic Programming Approach Spectrum Graph 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag/Wien 2005

Authors and Affiliations

  • S. Brunetti
    • 1
  • D. Dutta
    • 2
  • S. Liberatori
    • 3
  • E. Mori
    • 1
  • D. Varrazzo
    • 3
  1. 1.Dipartimento di Scienze Matematiche ed Informatiche “R. Magari”Università di SienaItaly
  2. 2.Department of Computer ScienceUniversity of Southern CaliforniaUSA
  3. 3.Dipartimento di Biologia MolecolareUniversità di SienaItaly

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