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Bioinformatics. 2005 Oct 15;21(20):3926-8. Epub 2005 Aug 18.

Structure clustering features on the Sfold Web server.

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  • 1Bioinformatics Center, Wadsworth Center, New York State Department of Health, Albany, 12208, USA.


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.



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