CARNAC: folding families of related RNAs
Laboratoire d'Informatique Fondamentale de Lille, UMR CNRS 8022, Université des Sciences et Technologies de Lille, France
* To whom correspondence should be addressed. Tel: +33 3 20 43 68 02; Fax: +33 3 20 43 65 66; Email: touzet{at}lifl.fr
Received February 13, 2004; Revised and Accepted April 2, 2004
We present a tool for the prediction of conserved secondary structure elements of a family of homologous non-coding RNAs. Our method does not require any prior multiple sequence alignment. Thus, it successfully applies to datasets with low primary structure similarity. The functionality is demonstrated using three example datasets: sequences of RNase P RNAs, ciliate telomerases and enterovirus messenger RNAs. CARNAC has a web server that can be accessed at the URL http://bioinfo.lifl.fr/carnac.
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