Table 3.

Web Resource for Predicting mRNA Secondary Structure

Software/Method	Input	Summary	Availability	References
Mfold	RNA sequence	It predicts the suboptimal structures within a free energy increment from the minimum free energy.	Software package and web server: http://mfold.rna.albany.edu/?q=mfold	89
RNAshapes	RNA sequence	It calculates shapes and their probabilities by analyzing the full ensemble, predicts the complete set of suboptimal structures and their probabilities	Software package and web server: http://bibiserv.techfak.uni-bielefeld.de/rnashapes/	90
RNAstructure	RNA sequence	It includes algorithms for RNA secondary structure prediction and calculation of base-pair probabilities.	Software package with GUI: http://rna.urmc.rochester.edu/RNAstructure.html	91
SFOLD	RNA sequence	It computes base pair probabilities from a representative sample of the full ensemble	Software package and web server: http://sfold.wadsworth.org/	75
Vienna package	RNA sequence	RNAfold: predicts MFE energy structure and base-pair probabilities RNAplfold: uses local folding to calculate base-pair probabilities	Software package: http://www.tbi.univie.ac.at/∼ivo/RNA/Web server: http://rna.tbi.univie.ac.at/	72 92