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Bioinformatics Advance Access published online on February 25, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm049
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Multiple structural alignment and clustering of RNA sequences

Elfar Torarinsson 1,2, Jakob H. Havgaard 1 and Jan Gorodkin 1,*

1 Division of Genetics and Bioinformatics, IBHV and Center for Bioinformatics, Faculty of Life Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
2 Department of Natural Sciences, Faculty of Life Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark

*To whom correspondence should be addressed. Jan Gorodkin, E-mail: gorodkin{at}bioinf.kvl.dk


  Abstract

Motivation: An apparent paradox in computational RNA structure prediction is that many methods, in advance, require a multiple alignment of a set of related sequences, when searching for a common structure between them. However, such a multiple alignment is hard to obtain even for few sequences with low sequence similarity without simultaneously folding and aligning them. Furthermore, it is of interest to conduct a multiple alignment of RNA sequence candidates found from searching as few as two genomic sequences.

Results: Here, based on the PMcomp program, we present a global multiple alignment program, FOLDALIGNM, which performs especially well on few sequences with low sequence similarity, and is comparable in performance with state of the art programs in general. In addition, it can cluster sequences based on sequence and structure similarity and output a multiple alignment for each cluster. Furthermore, preliminary results with local datasets indicate that the program is useful for post processing FOLDALIGN pairwise scans.

Availability: The program FOLDALIGNM is implemented in JAVA and is, along with some accompanying PERL scripts, available at http://foldalign.ku.dk/

Associate Editor: Dmitrij Frishman

Received on November 30, 2006; revised on January 16, 2007; accepted on February 6, 2007

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