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RNA secondary structure prediction using dynamic programming algorithm — A review and proposed work

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3 Author(s)
Mohd Nizam Osman ; School of Computer Sciences, University of Sciences Malaysia, 11800 Penang, Malaysia ; Rosni Abdullah ; Nuraini AbdulRashid

Ribonucleic acid (RNA) plays a fundamental and important role in cellular life forms and their function is directly related to their structure. RNA secondary structure prediction is a significant area of study for many scientists seeking insights into potential drug interactions or innovative new treatment methodologies. Predicting structure can overcome many issues related with physical structure determination and their study yields information useful in prediction of the full three dimensional structures and also in the interpretation of the biochemical abilities of the molecules. Therefore, predicting the secondary structure of RNA is very important for understanding their function. Furthermore, secondary structures are discrete and thus, well suited for computational methods. In this paper, we present a review on RNA secondary structure prediction using Dynamic Programming (DP) algorithm. An analysis of DP algorithm from previous work is discussed. We will present our proposed work for RNA secondary structure prediction using DP algorithm and special-purposed hardware of multicore and Graphical Processing Unit (GPU). We proposed to implement the DP algorithm approach on a hybrid of multicore and GPU platform to speed up the computational process of RNA secondary structure prediction.

Published in:

2010 International Symposium on Information Technology  (Volume:2 )

Date of Conference:

15-17 June 2010