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

International audienceBackground: 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

Jean-Jacques Auguste Chrétien, membre de la commune robespierriste

Certains éléments de la bourgeoisie aisée de la capitale, se sont engagés résolument dans la Révolution, même pendant sa période la plus radicale en l’an II Un itinéraire politique particulièrement révélateur et qui n’est peut-être pas exceptionnel, est celui de Jean-Jacques Auguste Chrétien. Fils de Jacques Fiacre Chrétien, maître doreur argenteur, et de Jeanne Oger, Jean-Jacques Auguste Chrétien naît vers 1758 à Paris. Son père travaille en association avec son frère Jean Chrétien, rue Bour..

Detecting MicroRNAs in Plant Genomes with miRkwood

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Les sangliers révélateurs des rapports entre acteurs d'un territoire. Le cas de Pays de Montbéliard Agglomération

The aim of this qualitative survey was to gain a better understanding of how relationships are formed between the players concerned by the expansion of wild boar populations in the Pays de Montbéliard Agglomération area. Collecting the views of hunters, farmers, elected representatives and environmentalists on the situation highlighted the existence of disagreements and/or different points of view. We therefore first sought to show how these players approached the evolution of the wild boar population. Noting that divergences appeared in the discourse of the various players, we then tried to pinpoint what the tensions were about. Beyond debates on the definition of the problem and its causes, it appears that the controversy goes far beyond the issue of wild boar population expansion, and that it is hunting and the role of hunters that are the subject of controversy.Cette enquête qualitative avait pour objectif de mieux comprendre comment les rapports se construisent entre les acteurs concernés par le phénomène d’expansion des populations de sangliers sur le territoire de Pays de Montbéliard Agglomération. Le recueil de discours sur la situation auprès de chasseurs, agriculteurs, élus et environnementalistes permet, à cet endroit, de souligner l’existence de désaccords et/ou différents points de vue. Aussi, nous avons tout d’abord cherché à montrer comment ces acteurs abordaient l’évolution de la population des sangliers. Constatant que des divergences apparaissaient dans les discours des uns et des autres, nous avons tenté, dans un second temps de repérer sur quoi portaient les crispations. Au-delà des débats sur la définition du problème et ses causes, il apparait que la controverse dépasse largement la problématique de l’expansion des populations de sangliers et que c’est bien la chasse et la place des chasseurs qui est sujet à polémique

Neural network models of cortical functions based on the computational properties of the cerebral cortex

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Direct and indirect cooperation between temporal and parietal networks for invariant visual recognition

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Finding and analysing microRNAs in plant genomes with miRkwood

National audienceMicroRNAs (miRNAs) play a crucial role in the post-transcriptional regulation of eukaryotic gene expression, in plants and animals. Many aspects of the biogenesis and evolution of miRNAs in animals and plants differ. For example, unlike miRNAs of animals, which are mainly found in introns or exons from coding genes, most plant miRNAs are encoded by discrete genes. Moreover, miRNAs are released from their precursors using distinct pathways in the two kingdoms. Also, miRNA precursors are more heterogeneous in plants than in animals, varying greatly in size and structure. These differences have justified dedicated approaches for miRNA gene finding. However although several prediction tools are available for metazoan genomes, the number of tools dedicated to plants is relatively limited. Considering this gap, we have developed miRkwood, a user-friendly web server specifically designed for plant miRNAs. miRkwood is able to face the diversity of plant pre-miRNAs and allows the prediction of precursors of both conserved and non-conserved miRNAs. Moreover, it offers an intuitive and comprehensive user interface to navigate in the data, as well as many export options (GFF, CSV, FASTA, ODT) to allow the user to conduct further analyses on a local computer. miRkwood can deal with both short genomic sequences (up to 100 000 nt) and full small RNA sequencing reads (provided that a BAM file is available). It is accessible at http://bioinfo.lifl.fr/mirkwoo