Automatic detection of conserved RNA structure elements in complete RNA virus genomes
Open Access
- 1 August 1998
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 26 (16) , 3825-3836
- https://doi.org/10.1093/nar/26.16.3825
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 ∼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
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