miRkwood: a tool for the reliable identification of microRNAs in plant genomes

Guigon, Isabelle; Legrand, Sylvain; Berthelot, Jean-Frédéric; Bini, Sébastien; Lanselle, Delphine; Benmounah, Mohcen; Touzet, Helene

Document type :

Article dans une revue scientifique: Article original

DOI :

10.1186/s12864-019-5913-9

Title :

miRkwood: a tool for the reliable identification of microRNAs in plant genomes

Author(s) :

Guigon, Isabelle [Auteur]
Plateforme de bioinformatique et de biostatistique de Lille - PLBS [Bilille]
Legrand, Sylvain [Auteur]

Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)]
Berthelot, Jean-Frédéric [Auteur]
Plateforme de bioinformatique et de biostatistique de Lille - PLBS [Bilille]
Bini, Sébastien [Auteur]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Lanselle, Delphine [Auteur]
Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 [Evo-Eco-Paléo (EEP)]
Benmounah, Mohcen [Auteur]
Plateforme de bioinformatique et de biostatistique de Lille - PLBS [Bilille]
Touzet, Helene [Auteur]

Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]

Journal title :

Bmc Genomics

Publisher :

BioMed Central

Publication date :

2019-12

ISSN :

1471-2164

English keyword(s) :

Plant genome
Micro-RNAs
Small RNA-seq
AGO-IP

HAL domain(s) :

Sciences du Vivant [q-bio]/Génétique/Génétique des populations [q-bio.PE]

English abstract : [en]

Background: MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulation of eukaryotic gene expression and are involved in many aspects of plant development. Although several prediction tools are available for ...
Show more >Background: MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulation of eukaryotic gene expression and are involved in many aspects of plant development. Although several prediction tools are available for metazoan genomes, the number of tools dedicated to plants is relatively limited. Results: Here, we present miRkwood, a user-friendly tool for the identification of miRNAs in plant genomes using small RNA sequencing data. Deep-sequencing data of Argonaute associated small RNAs showed that miRkwood is able to identify a large diversity of plant miRNAs and limits false positive predictions. Moreover, it outperforms current tools such as ShortStack and contrary to ShortStack, miRkwood provides a quality score allowing users to rank miRNA predictions. Conclusion: miRkwood is a very efficient tool for the annotation of miRNAs in plant genomes. It is available as a web server, as a standalone version, as a docker image and as a Galaxy tool:Show less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Internationale

Popular science :

Non

ANR Project :

Organisation et montée en puissance d'une Infrastructure Nationale de Génomique

Collections :

Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL

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