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Secondary Structure Prediction for Aligned RNA Sequences

Author

Listed:
  • Ivo l. Hofacker
  • Martin Fekete
  • Peter F. Stadler

Abstract

Most functional RNA molecules have characteristic secondary structures that are highly conserved in evolution. Here we present a method for computing the consensus structure of a set aligned RNA sequences taking into account both thermodynamic stability and sequence covariation. Comparison with phylogenetic structures of rRNAs shows that a reliability of prediction of more than 80% is achieved for only five related sequences. As an application we show that the Early Noduline mRNA contains significant secondary structure that is supported by sequence covariation.

Suggested Citation

  • Ivo l. Hofacker & Martin Fekete & Peter F. Stadler, 2001. "Secondary Structure Prediction for Aligned RNA Sequences," Working Papers 01-11-067, Santa Fe Institute.
    • Handle: RePEc:wop:safiwp:01-11-067
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