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Comparison of RNA Secondary Structure Prediction Tools in Predicting the Structure

Author Affiliations

  • 1 Department of Microbiology, Shree Ramkrishna Institute of Computer Education and Applied Sciences, Athwalines, Surat-395001, Gujarat, INDIA

Res. J. Recent Sci., Volume 3, Issue (IVC-2014), Pages 20-23, (2014)


Many numbers of software applications (GUIs) are available for the single stranded nucleic acid secondary structure prediction-like Mfold, CONTRA fold, IPknot, Compa RNA, Centroid Alifold, etc. Some uses Minimum Free Energy models (MFE) algorithm and others use stochastic context-free grammars (SCFGs), and rest rely on dynamic programming evolved as an alternative probabilistic methodology for modelling RNA structure. In contrast to physics-based methods, which are dependent on thousands of experimentally-measured thermodynamic parameters, SCFGs require fully-automated statistical learning algorithms to derive model parameters. The performance of 10 single-sequences from a numerous RNA sequences with respective methods were being evaluated. On the whole the most accurate and stable predictions obtained by single-sequence analyses are generated by Mfold, IPknot, RNA Structure and COFOLD.


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