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Bioinformatics Advance Access originally published online on December 4, 2008
Bioinformatics 2009 25(3):291-294; 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 2,3,4,5 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, 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 and 5Institute of Theoretical Chemistry, University of Vienna, Währingerstr. 17, A-1090 Vienna, Austria

*To whom correspondence should be addressed.


  Abstract

MicroRNAs (miRNAs) are a group of small, ~21 nt long, riboreg-ulators inhibiting gene expression at a post-transcriptional 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.

Availability: http://genome.ku.dk/resources/mirclust

Contact: gorodkin{at}genome.ku.dk

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded joint First Authors.

Associate Editor: Ivo Hofacker

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

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