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Nucleic Acids Research, Vol 26, Issue 16 3825-3836, Copyright © 1998 by Oxford University Press

ARTICLES

Automatic detection of conserved RNA structure elements in complete RNA virus genomes

IL Hofacker, M Fekete, C Flamm, MA Huynen, S Rauscher, PE Stolorz and PF Stadler
Institut fur Theoretische Chemie, Universitat Wien, Wien, Austria, EMBL, Heidelberg, Germany, Max Delbruck Center, Berlin, Germany.

We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and phylogenetic comparison. In contrast to purely phylogenetic methods, our algorithm can be used for small data sets of approximately 10 sequences, efficiently exploiting the information contained in the sequence variability. The procedure constructs a prediction only for those parts of sequences that are consistent with a single conserved structure. Our implementation produces reasonable consensus structures without user interference. As an example we have analysed the complete HIV-1 and hepatitis C virus (HCV) genomes as well as the small segment of hantavirus. Our method confirms the known structures in HIV-1 and predicts previously unknown conserved RNA secondary structures in HCV.
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