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

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Item Type:Article
Title:Automatic detection of conserved RNA structure elements in complete RNA virus genomes
Creators Name:Hofacker, I.L. and Fekete, M. and Flamm, C. and Huynen, M.A. and Rauscher, S. and Stolorz, P.E. and Stadler, P.F.
Abstract: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.
Keywords:Algorithms, Base Sequence, Consensus Sequence, Conserved Sequence, Hantavirus, Hepacivirus, HIV-1, Molecular Sequence Data, Nucleic Acid Conformation, Phylogeny, Thermodynamics, Viral Genome, Viral RNA
Source:Nucleic Acids Research
ISSN:0305-1048
Publisher:Oxford University Press (U.K.)
Volume:26
Number:16
Page Range:3825-3836
Date:15 August 1998
Official Publication:http://nar.oxfordjournals.org/cgi/content/abstract/26/16/3825
PubMed:View item in PubMed

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