Rapid ab initio RNA folding including pseudoknots via graph tree decomposition

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Rapid ab initio RNA folding including pseudoknots via graph tree decomposition (2006)

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by Jizhen Zhao , Russell L. Malmberg , Liming Cai

Venue:	IN PROCEEDINGS OF THE 6TH WORKSHOP ON ALGORITHMS IN BIOINFORMATICS (WABI
Citations:	4 - 0 self

BibTeX

@INPROCEEDINGS{Zhao06rapidab,
    author = {Jizhen Zhao and Russell L. Malmberg and Liming Cai},
    title = {Rapid ab initio RNA folding including pseudoknots via graph tree decomposition},
    booktitle = {IN PROCEEDINGS OF THE 6TH WORKSHOP ON ALGORITHMS IN BIOINFORMATICS (WABI},
    year = {2006},
    pages = {262--273},
    publisher = {}
}

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Abstract

The prediction of RNA secondary structure including pseudoknots remains a challenge due to the in-tractable computation of the sequence conformation from 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 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 optimal 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.

Keyphrases

rapid ab initio rna rna sequence set time-efficient algorithm optimal algorithm large number nucleotide interaction in-tractable computation efficient optimal algorithm efficient algorithm rna structure specialized maximum independent set corresponds sequence conformation diverse resource predicted rna structure tree decomposition high-degree polynomial time complexity optimal structure dynamic programming predicted structure rna secondary structure novel prediction technique new algorithm heuristic method heuristic algorithm graph tree decomposition overall sensitivity restricted class

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