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miRdentify: high stringency miRNA predictor identifies several novel animal miRNAs

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miRdentify : high stringency miRNA predictor identifies several novel animal miRNAs. / Hansen, Thomas B; Venø, Morten T; Kjems, Jørgen; Damgaard, Christian Kroun.

In: Nucleic Acids Research, Vol. 42, No. 16, e124, 22.07.2014, p. 1-11.

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@article{5f0ffc7ba4b340f0bfdde0d547825c76,
title = "miRdentify: high stringency miRNA predictor identifies several novel animal miRNAs",
abstract = "During recent years, miRNAs have been shown to play important roles in the regulation of gene expression. Accordingly, much effort has been put into the discovery of novel uncharacterized miRNAs in various organisms. miRNAs are structurally defined by a hairpin-loop structure recognized by the two-step processing apparatus, Drosha and Dicer, necessary for the production of mature ∼22-nucleotide miRNA guide strands. With the emergence of high-throughput sequencing applications, tools have been developed to identify miRNAs and profile their expression based on sequencing reads. However, as the read depth increases, false-positive predictions increase using established algorithms, underscoring the need for more stringent approaches. Here we describe a transparent pipeline for confident miRNA identification in animals, termed miRdentify. We show that miRdentify confidently discloses more than 400 novel miRNAs in humans, including the first male-specific miRNA, which we successfully validate. Moreover, novel miRNAs are predicted in the mouse, the fruit fly and nematodes, suggesting that the pipeline applies to all animals. The entire software package is available at www.ncrnalab.dk/mirdentify.",
author = "Hansen, {Thomas B} and Ven{\o}, {Morten T} and J{\o}rgen Kjems and Damgaard, {Christian Kroun}",
note = "{\circledC} The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.",
year = "2014",
month = "7",
day = "22",
doi = "10.1093/nar/gku598",
language = "English",
volume = "42",
pages = "1--11",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "16",

}

RIS

TY - JOUR

T1 - miRdentify

T2 - high stringency miRNA predictor identifies several novel animal miRNAs

AU - Hansen, Thomas B

AU - Venø, Morten T

AU - Kjems, Jørgen

AU - Damgaard, Christian Kroun

N1 - © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

PY - 2014/7/22

Y1 - 2014/7/22

N2 - During recent years, miRNAs have been shown to play important roles in the regulation of gene expression. Accordingly, much effort has been put into the discovery of novel uncharacterized miRNAs in various organisms. miRNAs are structurally defined by a hairpin-loop structure recognized by the two-step processing apparatus, Drosha and Dicer, necessary for the production of mature ∼22-nucleotide miRNA guide strands. With the emergence of high-throughput sequencing applications, tools have been developed to identify miRNAs and profile their expression based on sequencing reads. However, as the read depth increases, false-positive predictions increase using established algorithms, underscoring the need for more stringent approaches. Here we describe a transparent pipeline for confident miRNA identification in animals, termed miRdentify. We show that miRdentify confidently discloses more than 400 novel miRNAs in humans, including the first male-specific miRNA, which we successfully validate. Moreover, novel miRNAs are predicted in the mouse, the fruit fly and nematodes, suggesting that the pipeline applies to all animals. The entire software package is available at www.ncrnalab.dk/mirdentify.

AB - During recent years, miRNAs have been shown to play important roles in the regulation of gene expression. Accordingly, much effort has been put into the discovery of novel uncharacterized miRNAs in various organisms. miRNAs are structurally defined by a hairpin-loop structure recognized by the two-step processing apparatus, Drosha and Dicer, necessary for the production of mature ∼22-nucleotide miRNA guide strands. With the emergence of high-throughput sequencing applications, tools have been developed to identify miRNAs and profile their expression based on sequencing reads. However, as the read depth increases, false-positive predictions increase using established algorithms, underscoring the need for more stringent approaches. Here we describe a transparent pipeline for confident miRNA identification in animals, termed miRdentify. We show that miRdentify confidently discloses more than 400 novel miRNAs in humans, including the first male-specific miRNA, which we successfully validate. Moreover, novel miRNAs are predicted in the mouse, the fruit fly and nematodes, suggesting that the pipeline applies to all animals. The entire software package is available at www.ncrnalab.dk/mirdentify.

U2 - 10.1093/nar/gku598

DO - 10.1093/nar/gku598

M3 - Journal article

C2 - 25053842

VL - 42

SP - 1

EP - 11

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 16

M1 - e124

ER -