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Bioinformatics Advance Access published online on December 4, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn628
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Structural profiles of human miRNA families from pairwise clustering

Bogumil Kaczkowski 1,{dagger}, Elfar Torarinsson 1,{dagger}, Kristin Reiche 2, Jakob Hull Havgaard 1, Peter F. Stadler 3,2,4,5 and Jan Gorodkin 1,*

1Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Frederiksberg C, Denmark
2Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, Germany
3Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center of Bioinformatics, University of Leipzig, Härtelstrasse 16-18, Leipzig, Germany
4Santa Fe Institute, Santa Fe NM87501, USA
5Institute of Theoretical Chemistry, University of Vienna, Währingerstr. 17, A-1090 Vienna, Austria

*To whom correspondence should be addressed. Dr. Elfar Torarinsson, E-mail: elfar7{at}gmail.com


  Abstract

MicroRNAs are a group of small, ~21nt long, riboregulators inhibiting gene expression at a posttranscriptional level. Their most distinctive structural feature is the foldback hairpin of their precursor pre-miRNAs. Even though each pre-miRNA deposited in miRBase has its secondary structure already predicted, little is known about the patterns of structural conservation among pre-miRNAs. We address this issue by clustering the human pre-miRNA sequences based on pairwise, sequence and secondary structure alignment using FOLDALIGN, followed by global multiple alignment of obtained clusters by WAR. As a result, the common secondary structure was successfully determined for four FOLDALIGN clusters: the RF00027 structural family of the Rfam database and three clusters with previously undescribed consensus structures

Contact: gorodkin{at}genome.ku.dk

Associate Editor: Prof. Ivo Hofacker

{dagger}these authors contributed equally

Received on June 17, 2008; revised on December 1, 2008; accepted on December 2, 2008

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