Structural profiles of human miRNA families from pairwise clustering.
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.


BACKGROUND
http://genome.ku.dk/resources/mirclust
Kaczkowski
Bogumił
B
Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Frederiksberg C, Denmark.
Torarinsson
Elfar
E
Reiche
Kristin
K
Havgaard
Jakob Hull
JH
Stadler
Peter F
PF
Gorodkin
Jan
J
D001483:Base Sequence; D016000:Cluster Analysis; D019295:Computational Biology; D030541:Databases, Genetic; D015894:Genome, Human; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry* / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012984:Software
D035683:MicroRNAs