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Bioinformatics Vol. 19 no. 1 2003
Pages 108-116
© 2003 Oxford University Press

Finding the common structure shared by two homologous RNAs

O. Perriquet *, H. Touzet * and M. Dauchet

LIFL, UPRESA CNRS 8022, Batiment M3, Université des Sciences et Technologies de Lille, 59655 Villeneuve d’Ascq Cedex, France

Received on February 14, 2002 ; revised on May 7, 2002 and June 27, 2002 ; accepted on July 23, 2002

Motivation: CARNAC is a new method for pairwise folding of RNA sequences. The program takes into account local similarity, stem energy, and covariations to produce the common folding. It can handle all RNA types, and has also been adapted to align a new homologous sequence along a reference structured sequence.

Results: Using different data sets, we show that CARNAC provides a good partial prediction for a wide range of sequences (16S ssu rRNA, RNase P RNA, viruses) with only two sequences. In presence of a whole family of sequences, we also show that CARNAC can be used to detect whether the sequences actually share the same structure.

Availability: CARNAC is available at the URLhttp://www.lifl.fr/~perrique/rna/

Contact: perrique{at}lifl.fr; touzet{at}lifl.fr

* To whom correspondence should be addressed.


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