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Finding Common RNA Pseudoknot Structures in Polynomial Time

  • Patricia A. Evans
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4009)

Abstract

This paper presents the first polynomial time algorithm for finding common RNA substructures that include pseudoknots and similar structures. While a more general problem is known to be NP-hard, this algorithm exploits special features of RNA structures to match RNA bonds correctly in polynomial time. Although the theoretical upper bound on the algorithm’s time and space usage is high, the data-driven nature of its computation enables it to avoid computing unnecessary cases, dramatically reducing the actual running time. The algorithm works well in practice, and has been tested on sample RNA structures that include pseudoknots and pseudoknot-like tertiary structures.

Keywords

Polynomial Time Index Combination Common Substructure Pseudoknot Structure Turnip Yellow Mosaic Virus 
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 Berlin Heidelberg 2006

Authors and Affiliations

  • Patricia A. Evans
    • 1
  1. 1.Faculty of Computer ScienceUniversity of New BrunswickFrederictonCanada

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