Journal Article

Structural profiles of human miRNA families from pairwise clustering

Bogumił Kaczkowski, Elfar Torarinsson, Kristin Reiche, Jakob Hull Havgaard, Peter F. Stadler and Jan Gorodkin

in Bioinformatics

Volume 25, issue 3, pages 291-294
Published in print February 2009 | ISSN: 1367-4803
Published online December 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn628
Structural profiles of human miRNA families from pairwise clustering

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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@genome.ku.dk

Journal Article.  3374 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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