Abstract
BackgroundRNA secondary structure prediction is one major task in bioinformatics, and various computational methods have been proposed so far. Pseudoknot is one of the typical substructures appearing in several RNAs, and plays an important role in some biological processes. Prediction of RNA secondary structure with pseudoknots is still challenging since the problem is NP-hard when arbitrary pseudoknots are taken into consideration.ResultsWe introduce a new method of predicting RNA secondary structure with pseudoknots based on integer programming. In our formulation, we aim at minimizing the value of the objective function that reflects free energy of a folding structure of an input RNA sequence. We focus on a practical class of pseudoknots by setting constraints appropriately. Experimental results for a set of real RNA sequences show that our proposed method outperforms several existing methods in sensitivity. Furthermore, for a set of sequences of small length, our approach achieved good performance in both sensitivity and specificity.ConclusionOur integer programming-based approach for RNA structure prediction is flexible and extensible.
Highlights
RNA secondary structure prediction is one major task in bioinformatics, and various computational methods have been proposed so far
We present a new method of predicting RNA secondary structure with pseudoknots based on integer programming (IP)
We implemented the IP formulation by C++ and included the C++ optimization library provided by CPLEX on a machine with Intel Xeon CPU 5160 3.00 GHz and 8.00 GB RAM
Summary
RNA secondary structure prediction is one major task in bioinformatics, and various computational methods have been proposed so far. Prediction of RNA secondary structure with pseudoknots is still challenging since the problem is NP-hard when arbitrary pseudoknots are taken into consideration. Functional noncoding RNAs (ncRNAs) have been recognized as regulatory or catalytic molecules, and have received much attention in recent years. Due to difficulty in determining RNA 3D structure (tertiary structure) by experimental techniques, many attempts have so far been made at predicting secondary structure given an RNA sequence (primary structure). One of the fundamental secondary structures is shown, which is called a hairpin loop or stem loop. Another diagrammatic representation is arc depiction where base (page number not for citation purposes)
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