Abstract

The study about biological sequences is gaining momentum nowadays. An increasing number of researchers have proposed framework for the implementation of various algorithms for biomolecules sequence alignment and secondary structure prediction. A comparative study can also enhance the results but alignment and prediction algorithms vary widely in terms of both sensitivity and selectivity across different lengths and homologies. The independent benchmarking of these algorithms is rarely performed for siRNA sequences. Sequence alignment and determination of the secondary structure of biomolecules are very important for understanding their functions and behavior. This paper presents the implementation of Nussinov algorithm using Bio-Perl for the study of behavior of siRNA sequences.

References

• Crick, F. H. 1966. Codon – Anticodon Pairing: The Wobble Hypothesis. J. Mol. Biol. 19, 548–55.
• Eddy, S. R. 2004. How do RNA Folding Algorithms Works? Nature Bio-Technology, Vol. No. 22(11).
• Eddy, S. R. 2004. What is Dynamic Programming? Nature Biotechnology, Vol. 22, No. 7.
• Eddy, S. R. 1994. Durbin R.: RNA Sequence Analysis Using Covariance Models. Nucleic Acids Res, Vol. 22, 2079-2088.
• Gorodkin J, Heyer L. J., and, Stormo G. D. 1997. Finding the Most Significant Common Sequence and Structure Motifs in a Set of RNA Sequences. Nucl. Acids Res. 25, 3724-3732.
• Nussinov, R. et al. 1978. Algorithms for Loop Matching. SIAM Journal of Applied Mathematics, 35, 68–82.
• Nussinov, R. and Jacobson, A. 1980. Fast Algorithm for Predicting the Secondary Structure of Single-Stranded RNA. Proc Natl Acad. Sci. USA, 77, 6903-6910.
• Pipas, J., McMahon, J. 1975. Method for Predicting RNA Secondary Structure. Proc Natl. Acad Sci USA, 72.
• Tisdall James. 2001. Beginning Perl for Bioinformatics. Publisher: O'Reilly.
• Rivas E., Eddy S. R. 1999. A Dynamic Programming Algorithm for Biomolecules Structure Prediction Including Pseudoknots. Journal of Biomolecules of Molecular Biology, 285, 2053-2063.
• Hengwu Li, Daming Zhu. 2005. Algorithm for Predicting RNA Secondary Structure Including Pseudoknots. Journal of Communication and Computer, USA. 1548-7709.
• Goldgof Greg. 2004. RNA Secondary Structure Prediction and Runtime Optimization. Proceedings of Genome Informatics, Vol. 15, 473-478.
• Erlangung Zur. 2006. Prediction of Structural Non-Coding RNAs by Comparative Sequence Analysis. CLEI Electronic Journal, Vol. 8 No. 2.
• Sharma Gaurav, Ozgun Harmanci A. 2007. Probabilistic Methods for Improving Efficiency of RNA Secondary Structure Prediction across Multiple Sequences. IEEE, 34-38.
• Zhou Hong, Zeng Xiao. 2005. A Three-Phase Algorithm for Computer Aided siRNA Design. Informatica, 357–364.
• Wang Zhuozhi, Zhang Kaizhong. 2004. Multiple RNA Structure Alignment. Proceedings of the IEEE Computational Systems Bioinformatics Conference (CSB 2004).
• Dowell D. 2006. Efficient Pair-wise RNA Structure Prediction and Alignment Using Sequence Alignment Constraints. Journal of BMC Bioinformatics.