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Bioinformatics Advance Access published online on July 14, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti577
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received May 9, 2005
Revised June 16, 2005
Accepted July 6, 2005

Article

Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction

Jens Reeder 1 and Robert Giegerich 1*

1 Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany

* To whom correspondence should be addressed.
Robert Giegerich, E-mail: robert{at}TechFak.Uni-Bielefeld.DE


  Abstract

Motivation: The well-known Sankoff algorithm for simultaneous RNA sequence alignment and folding is currently considered an ideal, but computationally over-expensive method. Available tools implement this algorithm under various pragmatic restrictions. They are still costly to use, and it is difficult to judge if the moderate quality of results is due to the underlying model or to its imperfect implementation.

Results: We propose to re-define the consensus structure prediction problem in a way that does not imply a multiple sequence alignment step. For a family of RNA sequences, our method explicitly and independently enumerates the near-optimal abstract shape space, and predicts as the consensus an abstract shape common to all sequences. For each sequence, it delivers the thermodynamically best structure which has this common shape. As the shape space is much smaller than the structure space, and identification of common shapes can be done in linear time (in the number of shapes considered), the method is essentially linear in the number of sequences. Our evaluation shows that the new method compares favorably with available alternatives.

Availability: The new method has been implemented in the program RNAcast and is available on the Bielefeld Bioinformatics Server.


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