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Bioinformatics Advance Access originally published online on August 18, 2005
Bioinformatics 2005 21(20):3926-3928; doi:10.1093/bioinformatics/bti632
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

Structure clustering features on the Sfold Web server

Chi Yu Chan 1,*, Charles E. Lawrence 1,2 and Ye Ding 1

1Bioinformatics Center, Wadsworth Center, New York State Department of Health 150 New Scotland Avenue, Albany, NY 12208, USA
2Center for Computational Molecular Biology and Division of Applied Mathematics, Brown University 182 George Street, Providence, RI 02912, USA

*To whom correspondence should be addressed.

Summary: The energy landscape of RNA secondary structures is often complex, and the Boltzmann-weighted ensemble usually contains distinct clusters. Furthermore, the minimum free energy structure often lies outside of the cluster containing the structure determined by comparative sequence analysis. We have developed procedures to characterize and visualize the Boltzmann-weighted ensemble, and have made them available on the Sfold Web server. The new features on the Web server include clustering statistics, ensemble and cluster centroids, multi-dimensional scaling display and energy landscape representation of the Boltzmann-weighted ensemble.

Availability: http://sfold.wadsworth.org; http://www.bioinfo.rpi.edu/applications/sfold

Contact: chanc{at}wadsworth.org

Received on June 23, 2005; revised on August 12, 2005; accepted on August 15, 2005

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