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CentroidFold

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CentroidFold based on a generalized centroid estimator is one of the most accurate tools for predicting RNA secondary structures. See the original paper for the details of the algorithm.

CentroidFold Web Server
 
Link to the original paper
 
README for the software
 
Download
CentroidFold package contains three software: CentroidFold (RNA secondary structure prediction), CentroidAlifold (Common secondary structure prediction of RNAs) and CentroidHomfold (RNA secondary structure prediction with homologous sequences)
Figures
Each directory contains figures (PDF format) in the paper as follows: single: secondary structure predictions from an RNA sequence aln : common secondary structure predictions aln-n : common secondary structure predictions of 2,4,6,8,10 sequences
Help for Web Application
CentroidFold lets you get a predicted secondary structure for a given RNA sequence and a predicted common secondary structure for a given multiple-alignment.
Help Figures
 
ISMB2009
 

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