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Nucleic Acids Research 2005 33(Web Server Issue):W600-W604; doi:10.1093/nar/gki382
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© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

RNALOSS: a web server for RNA locally optimal secondary structures

P. Clote*

Department of Biology, Department of Computer Science (courtesy appointment) Higgins 355, Boston College, Chestnut Hill, MA 02467, USA

*Tel: +1 617 552 1332; Fax: +1 617 552 2011; Email: clote{at}bc.edu

Received February 14, 2005. Revised March 9, 2005. Accepted March 9, 2005.

RNAomics, analogous to proteomics, concerns aspects of the secondary and tertiary structure, folding pathway, kinetics, comparison, function and regulation of all RNA in a living organism. Given recently discovered roles played by micro RNA, small interfering RNA, riboswitches, ribozymes, etc., it is important to gain insight into the folding process of RNA sequences. We describe the web server RNALOSS, which provides information about the distribution of locally optimal secondary structures, that possibly form kinetic traps in the folding process. The tool RNALOSS may be useful in designing RNA sequences which not only have low folding energy, but whose distribution of locally optimal secondary structures would suggest rapid and robust folding. Website: http://clavius.bc.edu/~clotelab/RNALOSS/.


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