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Bioinformatics Advance Access published online on February 24, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti349
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received December 21, 2004
Revised February 8, 2005
Accepted February 20, 2005

Article

Predicting a set of minimal free energy RNA secondary structures common to two sequences

David H. Mathews 1*

1 Center for Human Genetics and Molecular Pediatric Disease, University of Rochester Medical Center, 601 Elmwood Avenue, Box 703, Rochester, NY 14642

* To whom correspondence should be addressed.
David H. Mathews, E-mail: David_Mathews{at}urmc.rochester.edu


  Abstract

Motivation: Function derives from structure; therefore there is need of methods for predicting functional RNA structures.

Results: The Dynalign algorithm, which predicts the lowest free energy secondary structure common to two unaligned RNA sequences, is extended to the prediction of a set of low energy structures. Dot plots can be drawn to show all base pairs in structures within an energy increment. Dynalign predicts more well-defined structures than structure prediction using a single sequence; in 5S rRNA sequences, the average number of base pairs in structures with energy within 20% of the lowest energy structure is 317 using Dynalign, but 569 using a single sequence. Structure prediction with Dynalign can also be constrained according to experiment or comparative analysis. The accuracy, measured as sensitivity and positive predictive value, of Dynalign is greater than predictions with a single sequence.

Availability: Dynalign can be downloaded at http://rna.urmc.rochester.edu.


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