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Parallel and Distributed Processing Symposium, International (2008)
Miami, FL, USA
Apr. 14, 2008 to Apr. 18, 2008
ISBN: 978-1-4244-1693-6
pp: 1-8
Ming-Ying Leung , Dept. of Math. Sciences and Bioinformatics Prog., The University of Texas at El Paso, USA
David Mireles , Dept. of Computer Science, The University of Texas at El Paso, USA
Michela Taufer , Dept. of Computer&Inf. Sciences, University of Delaware, USA
Thamar Solorio , Dept. of Computer of Science, The University of Texas at Dallas, USA
Abel Licon , Dept. of Computer&Inf. Sciences, University of Delaware, USA
ABSTRACT
Despite the computing power of emerging technologies, predicting long RNA secondary structures with thermodynamics-based methods is still infeasible, especially if the structures include complex motifs such as pseudoknots. This paper presents preliminary results on rebuilding RNA secondary structures by an extensive and systematic sampling of nucleotide chunks. The rebuilding approach merges the significant motifs found in the secondary structures of the single chunks. The extensive sampling and prediction of nucleotide chunks are supported by grid technology as part of the RNAVLab functionality. Significant motifs are identified in the chunk secondary structures and merged in a single structure based on their recurrences and other statistical insights. A critical analysis of the strengths, weaknesses, and future developments of our method is presented.
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CITATION
Ming-Ying Leung, David Mireles, Michela Taufer, Thamar Solorio, Abel Licon, "On the Effectiveness of Rebuilding RNA Secondary Structures from Sequence Chunks", Parallel and Distributed Processing Symposium, International, vol. 00, no. , pp. 1-8, 2008, doi:10.1109/IPDPS.2008.4536177
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