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Titel:
Automatic Detection of Conserved RNA Structure Elements
in Complete RNA Virus Genomes
Author(s):
Ivo L. Hofacker,
Martin Fekete,
Christoph Flamm,
Martijn A. Huynen,
Susanne Rauscher,
Paul E. Stolorz,
Peter F. Stadler
Appeared in:
Nucl. Acids Res., 26, 3825-2836 (1998)
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 about
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 analyzed
complete HIV-1 and Hepatitis C virus genomes as well as the small segment
of Hanta virus. Our method confirms the known structures in HIV-I and
predicts previously unknown conserved RNA secondary structures in HCV.
Keywords:
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