Structural profiles of human miRNA families from pairwise clustering

Bogumil Kaczkowski; Elfar Þórarinsson; Kristin Reiche; Jakob Hull Havgaard; Peter F. Stadler; Jan Gorodkin

doi:10.1093/bioinformatics/btn628

Structural profiles of human miRNA families from pairwise clustering

Bogumil Kaczkowski, Elfar Þórarinsson, Kristin Reiche, Jakob Hull Havgaard, Peter F. Stadler, Jan Gorodkin

Computational and RNA Biology

43 Citations (Scopus)

Abstract

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

Original language	English
Journal	Bioinformatics
Volume	25
Issue number	3
Pages (from-to)	291-294
Number of pages	4
ISSN	1367-4803
DOIs	https://doi.org/10.1093/bioinformatics/btn628
Publication status	Published - 2009

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title = "Structural profiles of human miRNA families from pairwise clustering",

abstract = "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. Availability: http://genome.ku.dk/resources/mirclust",

author = "Bogumil Kaczkowski and Elfar {\TH}{\'o}rarinsson and Kristin Reiche and Havgaard, {Jakob Hull} and Stadler, {Peter F.} and Jan Gorodkin",

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doi = "10.1093/bioinformatics/btn628",

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T1 - Structural profiles of human miRNA families from pairwise clustering

AU - Kaczkowski, Bogumil

AU - Þórarinsson, Elfar

AU - Reiche, Kristin

AU - Havgaard, Jakob Hull

AU - Stadler, Peter F.

AU - Gorodkin, Jan

PY - 2009

Y1 - 2009

N2 - 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. Availability: http://genome.ku.dk/resources/mirclust

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

U2 - 10.1093/bioinformatics/btn628

DO - 10.1093/bioinformatics/btn628

M3 - Journal article

C2 - 19059941

SN - 1367-4803

VL - 25

SP - 291

EP - 294

JO - Bioinformatics

JF - Bioinformatics

IS - 3

ER -

Structural profiles of human miRNA families from pairwise clustering

Abstract

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