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Bioinformatics Advance Access first published online on June 21, 2005
This version published online on June 21, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti550
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received April 1, 2005
Revised June 16, 2005
Accepted June 16, 2005

Article

MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons

Sven Siebert 1 and Rolf Backofen 1*

1 Department of Bioinformatics, Institute of Computer Science, Friedrich-Schiller-University Jena, Ernst-Abbe Platz 2, 07743 Jena, Germany

* To whom correspondence should be addressed.
Rolf Backofen, E-mail: backofen{at}inf.uni-jena.de


  Abstract

Motivation: Due to the importance of considering secondary structures in aligning functional RNAs, several pairwise sequence-structure alignment methods have been developed. They use extended alignment scores that evaluate secondary structure information in addition to sequence information. However, two problems for the multiple alignment step remain. First, how to combine pairwise sequence-structure alignments into a multiple alignment and second, how to generate secondary structure information for sequences where explicit structural information is missing.

Results: We describe a novel approach for multiple alignment of RNAs (MARNA) taking into consideration both the primary sequences and the secondary structures. It is based on pairwise sequence-structure comparisons of RNAs. From these sequence-structure alignments, libraries of weighted alignment edges are generated. The weights reflect the sequential and structural conservation. For sequences where secondary structures are missing, the libraries are generated by sampling low energy conformations. The libraries are then processed by the T-Coffee system (Notredame et al., 2000), which is a consistency based multiple alignment method. Furthermore, we are able to extract a consensus-sequence and -structure from a multiple alignment. We have successfully tested MARNA on several datasets taken from the Rfam database.

Availability: MARNA can be used online on our webpage www.bio.inf.uni-jena.de/Software/MARNA/index.html.


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