Structural profiles of human miRNA families from pairwise clustering

B. Kaczkowski, E. Torarinsson, K. Reiche, J. H. Havgaard, P. F. Stadler, J. Gorodkin
2008 Bioinformatics  
MicroRNAs (miRNAs) are a group of small, ∼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
more » ... econdary 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.
doi:10.1093/bioinformatics/btn628 pmid:19059941 fatcat:ctkvuhpm4fbd3kntx3kahnzcry