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Nucleic Acids Research Advance Access published online on May 12, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp367
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Web Server Issue

CENTROIDFOLD: a web server for RNA secondary structure prediction

Kengo Sato1,2,*, Michiaki Hamada2,3, Kiyoshi Asai2,4 and Toutai Mituyama2

1Japan Biological Informatics Consortium (JBIC), 2–45 Aomi, Koto-ku, Tokyo 135–8073, 2Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2–42 Aomi, Koto-ku, Tokyo 135–0064, 3Mizuho Information & Research Institute, Inc., 2–3 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101–8443 and 4Graduate School of Frontier Sciences, University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa 277–8562, Japan

*To whom correspondence should be addressed. Tel: +81 3 3599 8743; Fax: +81 3 3599 8081; Email: sato-kengo{at}aist.go.jp

Received January 30, 2009. Revised April 11, 2009. Accepted April 24, 2009.

The CENTROIDFOLD web server (http://www.ncrna.org/centroidfold/) 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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