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Bioinformatics Vol. 16 no. 11 2000
Pages 1042-1043
© 2000 Oxford University Press

Applications Note

Circles: automating the comparative analysis of RNA secondary structure

Roderic D.M. Page 1

1 Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, UK

Received on May 21, 2000 ; revised on July 4, 2000 ; accepted on July 7, 2000

Summary: Circles is a program for inferring RNA secondary structure using maximum weight matching. The program can read in an alignment in FASTA, ClustalW, or NEXUS format, compute a maximum weight matching, and export one or more secondary structures in various file formats.

Availability: The program is available at no cost from http://taxonomy.zoology.gla.ac.uk/rod/circles/ and requires Windows 95/98/NT.

Contact: r.page{at}bio.gla.ac.uk


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