Nucleic Acids Research, 2003, Vol. 31, No. 13 3429-3431
© 2003 Oxford University Press
Vienna RNA secondary structure server
Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Währingerstraße 17, A-1090 Wien, Austria
*Tel: +43 1 4277 52738; Fax: +43 1 4277 52793; Email: ivo{at}tbi.univie.ac.at
The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently offers prediction of secondary structure from a single sequence, prediction of the consensus secondary structure for a set of aligned sequences and the design of sequences that will fold into a predefined structure. All three services can be accessed via the Vienna RNA web server at http://rna.tbi.univie.ac.at/.
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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