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Rapid ab initio RNA Folding Including Pseudoknots Via Graph Tree Decomposition

  • Jizhen Zhao
  • Russell L. Malmberg
  • Liming Cai
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4175)

Abstract

The prediction of RNA secondary structure including pseudoknots remains a challenge due to the intractable computation of the sequence conformation from intriguing nucleotide interactions. Optimal algorithms often assume a restricted class for the predicted RNA structures and yet still require a high-degree polynomial time complexity, which is too expensive to use. Heuristic methods may yield time-efficient algorithms but they do not guarantee optimality of the predicted structure. This paper introduces a new and efficient algorithm for the prediction of RNA structure with pseudoknots for which the structure is not restricted. Novel prediction techniques are developed based on graph tree decomposition. In particular, stem overlapping relationships are defined with a graph, in which a specialized maximum independent set (IS) corresponds to the desired optimal structure. Such a graph is tree decomposable; dynamic programming over a tree decomposition of the graph leads to an efficient algorithm. The new algorithm is evaluated on a large number of RNA sequence sets taken from diverse resources. It demonstrates overall sensitivity and specificity that outperforms or is comparable with those of previous optimal and heuristic algorithms yet it requires significantly less time than other optimal algorithms.

Keywords

Tree Decomposition Hepatitis Delta Virus Tree Width Thermodynamic Energy Dynamic Programming Table 
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

  • Jizhen Zhao
    • 1
  • Russell L. Malmberg
    • 2
  • Liming Cai
    • 1
  1. 1.Department of Computer ScienceUniversity of GeorgiaAthensUSA
  2. 2.Department of Plant BiologyUniversity of GeorgiaAthensUSA

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