Structure clustering features on the Sfold Web server

Authors:
Chi Yu Chan;Charles E. Lawrence;Ye Ding
Affiliations:
Bioinformatics Center, Wadsworth Center, New York State Department of Health 150 New Scotland Avenue, Albany, NY 12208, USA;Bioinformatics Center, Wadsworth Center, New York State Department of Health 150 New Scotland Avenue, Albany, NY 12208, USA;Bioinformatics Center, Wadsworth Center, New York State Department of Health 150 New Scotland Avenue, Albany, NY 12208, USA
Venue:
Bioinformatics
Year:
2005

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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 display and energy landscape representation of the Boltzmann-weighted ensemble. Availability:http://sfold.wadsworth.org; http://www.bioinfo.rpi.edu/applications/sfold Contact: chanc@wadsworth.org