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Nucleic Acids Research, 2003, Vol. 31, No. 13 3416-3422
© 2003 Oxford University Press

RNAsoft: a suite of RNA secondary structure prediction and design software tools

Mirela Andronescu, Rosalía Aguirre-Hernández, Anne Condon* and Holger H. Hoos

Department of Computer Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada

*To whom correspondence should be addressed: Tel: +1 6048228175; Fax: +1 604 822 5485; Email: condon{at}cs.ubc.ca

DNA and RNA strands are employed in novel ways in the construction of nanostructures, as molecular tags in libraries of polymers and in therapeutics. New software tools for prediction and design of molecular structure will be needed in these applications. The RNAsoft suite of programs provides tools for predicting the secondary structure of a pair of DNA or RNA molecules, testing that combinatorial tag sets of DNA and RNA molecules have no unwanted secondary structure and designing RNA strands that fold to a given input secondary structure. The tools are based on standard thermodynamic models of RNA secondary structure formation. RNAsoft can be found online at http://www.RNAsoft.ca.


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