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Bioinformatics. 2009 Feb 1;25(3):291-4. doi: 10.1093/bioinformatics/btn628. Epub 2008 Dec 4.

Structural profiles of human miRNA families from pairwise clustering.

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  • 1Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Frederiksberg C, Denmark.


MicroRNAs (miRNAs) are a group of small, approximately 21 nt long, riboregulators 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.


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