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Nucleic Acids Res. 2009 Jul;37(Web Server issue):W277-80. doi: 10.1093/nar/gkp367. Epub 2009 May 12.

CENTROIDFOLD: a web server for RNA secondary structure prediction.

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Japan Biological Informatics Consortium, 2-45 Aomi, Koto-ku, Tokyo 135-8073, Japan.


The CENTROIDFOLD web server ( is a web application for RNA secondary structure prediction powered by one of the most accurate prediction engine. The server accepts two kinds of sequence data: a single RNA sequence and a multiple alignment of RNA sequences. It responses with a prediction result shown as a popular base-pair notation and a graph representation. PDF version of the graph representation is also available. For a multiple alignment sequence, the server predicts a common secondary structure. Usage of the server is quite simple. You can paste a single RNA sequence (FASTA or plain sequence text) or a multiple alignment (CLUSTAL-W format) into the textarea then click on the 'execute CentroidFold' button. The server quickly responses with a prediction result. The major advantage of this server is that it employs our original CentroidFold software as its prediction engine which scores the best accuracy in our benchmark results. Our web server is freely available with no login requirement.

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