compPknots: A Framework for Parallel Prediction and Comparison of RNA Secondary Structures with Pseudoknots
Codes for RNA secondary structure prediction based on energy minimization are usually time and resource intensive. For this reason several codes have been simplified: in some cases they do not predict complex structures like pseudoknots, other times they predict structures with reduced lengths, or with simple pseudoknots. Each of these codes has its strengths and weaknesses. Providing scientists with tools that combine the strengths of the several codes is a worthwhile objective. To address this need, we present compPknots, a parallel framework that uses a combination of existing codes like Pknots-RE and Pknots-RG, to predict RNA secondary structures concurrently and automatically compare them with reference structures from databases or literature. In this paper compPknots is used to compare the predictions of 217 RNA structures from the PseudoBase database. Its parallel master-slave architecture provide scientists with higher prediction accuracies in shorter time.
KeywordsSecondary Structure Single Code Dynamic Programming Procedure Parallel Framework Input Segment
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- 5.Reeder, J., Giegerich, R.: Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics 5(104) (2004)Google Scholar
- 7.Batenburg, F.H.D., van Gultyaev, A.P., Pleij, C.W.A., Ng, J., Oliehoek, J.: Pseudobase: a Database with RNA Pseudoknots. Nucl. Acids Res. 28(1) (2000)Google Scholar
- 8.Bidou, L., Stahl, G., Grima, B., Liu, H., Cassan, M., Rousset, J.: In Vivo HIV-I Frameshifting Efficiency is Directly Related to the Stability of the Stem-loop Stimulatory Signal. RNA 3, 1153–1158 (1997)Google Scholar
- 11.Uemura, Y., Hasegawa, A., Kobayashi, S., Yokomori: Grammatically Modeling and Predicting RNA Secondary Structures. In: Proceedings of the Genome Informatics Workshop, pp. 67–76. Universal Academy Press, Tokyo (1995)Google Scholar
- 13.Estrada, T., Licon, A., Taufer, M.: CompPknots: a Framework for Parallel Prediction and Comparison of RNA Secondary Structures with Pseudoknots. Technical Report UTEP-CS-06-42, University of Texas, El Paso (September 2006)Google Scholar
- 14.Gardner, P.P., Giegerich, R.: A Comprehensive Comparison of Comparative RNA Structure Prediction Approaches. BMC Bioinformatics 5(140) (2004)Google Scholar