title: plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants.
abstract: High-throughput sequencing techniques have made it possible to assay an organism's entire repertoire of small non-coding RNAs (ncRNAs) in an efficient and cost-effective manner. The moderate size of small RNA-seq datasets makes it feasible to provide free web services to the research community that provide many basic features of a small RNA-seq analysis, including quality control, read normalization, ncRNA quantification, and the prediction of putative novel ncRNAs. DARIO is one such system that so far has been focussed on animals. Here we introduce an extension of this system to plant short non-coding RNAs (sncRNAs). It includes major modifications to cope with plant-specific sncRNA processing. The current version of plantDARIO covers analyses of mapping files, small RNA-seq quality control, expression analyses of annotated sncRNAs, including the prediction of novel miRNAs and snoRNAs from unknown expressed loci and expression analyses of user-defined loci. At present Arabidopsis thaliana, Beta vulgaris, and Solanum lycopersicum are covered. The web tool links to a plant specific visualization browser to display the read distribution of the analyzed sample. The easy-to-use platform of plantDARIO quantifies RNA expression of annotated sncRNAs from different sncRNA databases together with new sncRNAs, annotated by our group. The plantDARIO website can be accessed at http://plantdario.bioinf.uni-leipzig.de/.
authors.affiliation: Institut für Informatik, Martin-Luther-Universität Halle-Wittenberg Halle (Saale), Germany ; Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University Leipzig Leipzig, Germany.
authors.forename: Deblina
authors.initials: D
authors.lastname: Patra
authors.affiliation: Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University Leipzig Leipzig, Germany ; ecSeq Bioinformatics Leipzig, Germany.
authors.forename: Mario
authors.initials: M
authors.lastname: Fasold
authors.affiliation: Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University Leipzig Leipzig, Germany ; ecSeq Bioinformatics Leipzig, Germany.
authors.forename: David
authors.initials: D
authors.lastname: Langenberger
authors.affiliation: Institut für Pysikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Steger
authors.affiliation: Institut für Informatik, Martin-Luther-Universität Halle-Wittenberg Halle (Saale), Germany ; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig, Germany.
authors.forename: Ivo
authors.initials: I
authors.lastname: Grosse
authors.affiliation: Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University Leipzig Leipzig, Germany ; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig, Germany ; Max Planck Institute for Mathematics in the Sciences Leipzig, Germany ; Fraunhofer Institute for Cell Therapy and Immunology Leipzig, Germany ; Department of Theoretical Chemistry of the University of Vienna Vienna, Austria ; Center for RNA in Technology and Health, University of Copenhagen Frederiksberg, Denmark ; Santa Fe Institute Santa Fe, USA.
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
keywords: expression analysis; high-throughput sequencing; microRNA; ncRNAome; non-coding RNA; snoRNA; tRNA