Approximation Algorithms for Predicting RNA Secondary Structures with Arbitrary Pseudoknots

  • Authors:

  • Minghui Jiang

  • Affiliations:

  • Utah State University, Logan

  • Venue:
  • IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
  • Year:
  • 2010

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Abstract

We study three closely related problems motivated by the prediction of RNA secondary structures with arbitrary pseudoknots: the problem 2-Interval Pattern proposed by Vialette [CHECK END OF SENTENCE], the problem Maximum Base Pair Stackings proposed by Leong et al. [CHECK END OF SENTENCE], and the problem Maximum Stacking Base Pairs proposed by Lyngsø [CHECK END OF SENTENCE]. For the 2-Interval Pattern, we present polynomial-time approximation algorithms for the problem over the preceding-and-crossing model and on input with the unitary restriction. For Maximum Base Pair Stackings and Maximum Stacking Base Pairs, we present polynomial-time approximation algorithms for the two problems on explicit input of candidate base pairs. We also propose a new problem called Length-Weighted Balanced 2-Interval Pattern, which is natural in the context of RNA secondary structure prediction.