Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes

Ivo L. Hofacker, Martin Fekete, Christoph Flamm, Martijn A. Huynen, Susanne Rauscher, Paul E. Stolorz and Peter F. Stadler
Additional contact information
Peter F. Stadler: http://www.santafe.edu/~stadler

Working Papers from Santa Fe Institute

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: RNA folding; conserved secondary structures; RNA viruses (search for similar items in EconPapers)
Date: 1998-02
References: View complete reference list from CitEc
Citations: View citations in EconPapers (3)

There are no downloads for this item, see the EconPapers FAQ for hints about obtaining it.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:wop:safiwp:98-02-020

Access Statistics for this paper

More papers in Working Papers from Santa Fe Institute Contact information at EDIRC.
Bibliographic data for series maintained by Thomas Krichel ().