On the Complexity of Protein Similarity Search under mRNA Structure Constraints

  • Rolf Backofen
  • N.S. Narayanaswamy
  • Firas Swidan
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2285)


This paper addresses the complexity of a new problem associated with RNA secondary structure prediction. The issue is to identify an mRNA which has the secondary structure (=set of bonds) of a given mRNA, and the amino acid sequence it encodes has maximum similarity( defined below) to a given amino acid sequence. The problem is modeled as an optimization problem and a linear time algorithm is presented for the case when the given mRNA has a hairpin like secondary structure. Relevant extensions of this problem are shown to be NP-complete, and a factor 2 approximation algorithm is designed for the problem instances generated by the NP-completeness reduction.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2002

Authors and Affiliations

  • Rolf Backofen
    • 1
  • N.S. Narayanaswamy
    • 1
  • Firas Swidan
    • 1
  1. 1.Institut für InformatikMunichGermany

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