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Bioinformatics Advance Access published online on August 18, 2005
Bioinformatics, 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@oupjournals.org
Received June 23, 2005
Revised August 12, 2005
Accepted August 15, 2005

Applications note

Structure clustering features on the Sfold Web server

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

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

* To whom correspondence should be addressed.
Chi Yu Chan, E-mail: chanc{at}wadsworth.org


  Abstract

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 (MDS) display, and energy landscape representation of the Boltzmann-weighted ensemble.

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


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