Structural profiles of human miRNA families from pairwise clustering

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Structural profiles of human miRNA families from pairwise clustering. / Kaczkowski, Bogumil; Þórarinsson, Elfar; Reiche, Kristin; Havgaard, Jakob Hull; Stadler, Peter F.; Gorodkin, Jan.

In: Bioinformatics, Vol. 25, No. 3, 2009, p. 291-294.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Kaczkowski, B, Þórarinsson, E, Reiche, K, Havgaard, JH, Stadler, PF & Gorodkin, J 2009, 'Structural profiles of human miRNA families from pairwise clustering', Bioinformatics, vol. 25, no. 3, pp. 291-294. https://doi.org/10.1093/bioinformatics/btn628

APA

Kaczkowski, B., Þórarinsson, E., Reiche, K., Havgaard, J. H., Stadler, P. F., & Gorodkin, J. (2009). Structural profiles of human miRNA families from pairwise clustering. Bioinformatics, 25(3), 291-294. https://doi.org/10.1093/bioinformatics/btn628

Vancouver

Kaczkowski B, Þórarinsson E, Reiche K, Havgaard JH, Stadler PF, Gorodkin J. Structural profiles of human miRNA families from pairwise clustering. Bioinformatics. 2009;25(3):291-294. https://doi.org/10.1093/bioinformatics/btn628

Author

Kaczkowski, Bogumil ; Þórarinsson, Elfar ; Reiche, Kristin ; Havgaard, Jakob Hull ; Stadler, Peter F. ; Gorodkin, Jan. / Structural profiles of human miRNA families from pairwise clustering. In: Bioinformatics. 2009 ; Vol. 25, No. 3. pp. 291-294.

Bibtex

@article{25225690214d11df8ed1000ea68e967b,
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",
year = "2009",
doi = "10.1093/bioinformatics/btn628",
language = "English",
volume = "25",
pages = "291--294",
journal = "Computer Applications in the Biosciences",
issn = "1471-2105",
publisher = "Oxford University Press",
number = "3",

}

RIS

TY - JOUR

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

VL - 25

SP - 291

EP - 294

JO - Computer Applications in the Biosciences

JF - Computer Applications in the Biosciences

SN - 1471-2105

IS - 3

ER -

ID: 18203385