title: sRNAtoolbox: an integrated collection of small RNA research tools.
abstract: Small RNA research is a rapidly growing field. Apart from microRNAs, which are important regulators of gene expression, other types of functional small RNA molecules have been reported in animals and plants. MicroRNAs are important in host-microbe interactions and parasite microRNAs might modulate the innate immunity of the host. Furthermore, small RNAs can be detected in bodily fluids making them attractive non-invasive biomarker candidates. Given the general broad interest in small RNAs, and in particular microRNAs, a large number of bioinformatics aided analysis types are needed by the scientific community. To facilitate integrated sRNA research, we developed sRNAtoolbox, a set of independent but interconnected tools for expression profiling from high-throughput sequencing data, consensus differential expression, target gene prediction, visual exploration in a genome context as a function of read length, gene list analysis and blast search of unmapped reads. All tools can be used independently or for the exploration and downstream analysis of sRNAbench results. Workflows like the prediction of consensus target genes of parasite microRNAs in the host followed by the detection of enriched pathways can be easily established. The web-interface interconnecting all these tools is available at http://bioinfo5.ugr.es/srnatoolbox.
authors.affiliation: Genomics and Bioinformatics Platform of Andalusia (GBPA), Edificio INSUR, Calle Albert Einstein, 41092-Sevilla, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Rueda
authors.affiliation: Centro de Genómica e Investigaciones Oncológicas, Pfizer-Universidad de Granada-Junta de Andalucía, Granada 18016, Spain.
authors.forename: Guillermo
authors.initials: G
authors.lastname: Barturen
authors.affiliation: Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada, Spain Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Lebrón
authors.affiliation: Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada, Spain Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain.
authors.forename: Cristina
authors.initials: C
authors.lastname: Gómez-Martín
authors.affiliation: Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada, Spain Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain.
authors.forename: Ángel
authors.initials: Á
authors.lastname: Alganza
authors.affiliation: Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada, Spain Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain.
authors.forename: José L
authors.initials: JL
authors.lastname: Oliver
authors.affiliation: Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada, Spain Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain hackenberg@ugr.es.
authors.forename: Michael
authors.initials: M
authors.lastname: Hackenberg
mesh_terms: D020869:Gene Expression Profiling; D006801:Humans; D020407:Internet; D035683:MicroRNAs / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000378:metabolism*; D012984:Software
chemical_list: D035683:MicroRNAs; D058727:RNA, Small Untranslated