Finding the common structure shared by two homologous RNAs.
BACKGROUND
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.


BACKGROUND
CARNAC is available at the URLhttp://www.lifl.fr/~perrique/rna/.
Perriquet
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LIFL, UPRESA CNRS 8022, Bâtiment M3, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq Cedex, France. perrique@lifl.fr
Touzet
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Dauchet
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D000465:Algorithms; D003580:Cytochromes / Q000235:genetics; D030561:Databases, Nucleic Acid; D004722:Endoribonucleases / Q000235:genetics; D004770:Enterovirus / Q000235:genetics; D008957:Models, Genetic; D015233:Models, Statistical; D012313:RNA / Q000235:genetics; D016337:RNA, Catalytic / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics; D043262:Ribonuclease P; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid
D003580:Cytochromes; D016337:RNA, Catalytic; D012333:RNA, Messenger; D012336:RNA, Ribosomal, 16S; D012367:RNA, Viral; D012313:RNA; D004722:Endoribonucleases; D043262:Ribonuclease P