The week's pick
Reseach Article
Prediction of RNA Secondary Structure from Random Sequences using ZEM
| International Journal of Computer Applications |
| Foundation of Computer Science (FCS), NY, USA |
| Volume 42 - Number 10 |
| Year of Publication: 2012 |
| Authors: Cinita Mary Mathew, Meera Krishna G H, G Gopakumar |
10.5120/5728-7796
|
Cinita Mary Mathew, Meera Krishna G H, G Gopakumar . Prediction of RNA Secondary Structure from Random Sequences using ZEM. International Journal of Computer Applications. 42, 10 ( March 2012), 15-19. DOI=10.5120/5728-7796
Abstract
The biological role of many RNA crucially depends on their structure. The in depth understanding of the secondary structure of RNA would provide a better insight in to their functionality. Predicting secondary structure of RNA is the most important factor in determining its 3d structure and functions. This work proposes a model for exploring the features of a number of RNA sequences simultaneously so that comparison of sequences can be made and relevant sequences can be identified. The proposed model accepts RNA sequences in any valid biological file format. For each given sequence, required number of random sequences is generated. The generated sequences should have the same base composition as that of original sequence. ZEM (Zuker's Energy Minimization) Algorithm finds the biologically correct structure of each RNA sequence and its corresponding free energy value. The proposed prototype enables us to experiment with a number of RNA sequences and to study their features so that biologically relevant inferences can be made. An important area where it finds application is in the design of pharmaceutical products.
References
- Mirela Andronescu et. al "A New Algorithm for RNA Secondary Structure Design", Journal of Molecular Biology, Volume 336,Isuue3 20 February 2004
- Amy C. Anderson "The Process of Structure-Based Drug Design", Chemistry & Biology, Vol. 10, 787–797, September, 2003
- Rune B. Lyngs Michael Zuker, Christian N. S. Pedersen "Internal loops in RNA secondary structure prediction", Proceedings of the 3th Annual nternational Conference on Computational Molecular Biology (RECOMB)
- M. Zuker, D. H. Mathews & D. H. Turner, "Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide". In RNA Biochemistry and Biotechnology, J. Barciszewski & B. F. C. Clark, eds. , NATO ASI Series, Kluwer Academic Publishers, (1999)
- M. Zuker "Prediction of RNA Secondary Structure by Energy Minimization". in Computer Analysis of Sequence Data A. M. Griffin and H. G. Griffin eds. Methods in Molecular Biology, Humana Press Inc. , 267-294 (1994).
- Ruth Nussinov and Ann B. Jacobson, "Fast algorithm for predicting the secondary structure of single stranded RNA". Proc. Natl. Acad. Sci. USA, 77(11):6309
- N Gautham , "BioInformatics Databases and Algorithms", Narosa Publishing House.
- R. Durbin, S. Eddy "Biological Sequence Analysis", Cambridge University Press Inc.
- Lisa Yu, "Study of RNA Secondary Structure Prediction Algorithms".
- Rivas E. , Eddy S. R. , "A Dynamic Programming Algorithm for RNA Structure. Prediction Including Pseudoknots", Academic Press, 1999.
- RNA structure determination Experimental techniques & Computational prediction [PDF document]. Retrieved from http://www. ibi. vu. nl/teaching/masters/prot_struc/2008/ps-lec12-2008. pdf
- D. Huson, "Algorithms in Bioinformatics I", WS'06, ZBIT, December 6, 2006
- The web interface to the RNAfold program can be found at http://rna. tbi. univie. ac. at/cgi-bin/RNAfold. cgi
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