miRkwood: a tool for the reliable identification of microRNAs in plant genomes - Archive ouverte HAL Accéder directement au contenu
Article Dans Une Revue BMC Genomics Année : 2019

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

(1) , (2) , (1) , (3) , (2) , (1) , (3)
1
2
3

Résumé

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:
Fichier principal
Vignette du fichier
Guigon et al. - 2019 - BMC Genomics.pdf (1.39 Mo) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte
Loading...

Dates et versions

hal-02265367 , version 1 (09-08-2019)

Identifiants

Citer

Isabelle Guigon, Sylvain Legrand, Jean-Frédéric Berthelot, Sébastien Bini, Delphine Lanselle, et al.. miRkwood: a tool for the reliable identification of microRNAs in plant genomes. BMC Genomics, 2019, 20 (1), ⟨10.1186/s12864-019-5913-9⟩. ⟨hal-02265367⟩
115 Consultations
92 Téléchargements

Altmetric

Partager

Gmail Facebook Twitter LinkedIn More