title: iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data.
abstract: The interest in investigating the biological roles of small non-coding RNAs (sncRNAs) is increasing, due to the pleiotropic effects of these molecules exert in many biological contexts. While several methods and tools are available to study microRNAs (miRNAs), only few focus on novel classes of sncRNAs, in particular PIWI-interacting RNAs (piRNAs). To overcome these limitations, we implemented iSmaRT ( i ntegrative Sm all R NA T ool-kit), an automated pipeline to analyze smallRNA-Seq data.
  
  
  
  iSmaRT is a collection of bioinformatics tools and own algorithms, interconnected through a Graphical User Interface (GUI). In addition to performing comprehensive analyses on miRNAs, it implements specific computational modules to analyze piRNAs, predicting novel ones and identifying their RNA targets. A smallRNA-Seq dataset generated from brain samples of Huntington's Disease patients was used here to illustrate iSmaRT performances, demonstrating how the pipeline can provide, in a rapid and user friendly way, a comprehensive analysis of different classes of sncRNAs. iSmaRT is freely available on the web at ftp://labmedmolge-1.unisa.it (User: iSmart - Password: password).
  
  
  
  aweisz@unisa.it or ggiurato@unisa.it.
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.|Department of Molecular Biotechnology and Health Sciences, University of Torino, via Nizza 52, Torino, Italy.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Panero
authors.affiliation: Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.
authors.forename: Antonio
authors.initials: A
authors.lastname: Rinaldi
authors.affiliation: Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.
authors.forename: Domenico
authors.initials: D
authors.lastname: Memoli
authors.affiliation: Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.|Genomix4Life, University of Salerno, Baronissi, SA, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Nassa
authors.affiliation: Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.
authors.forename: Maria
authors.initials: M
authors.lastname: Ravo
authors.affiliation: Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Rizzo
authors.affiliation: Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.
authors.forename: Roberta
authors.initials: R
authors.lastname: Tarallo
authors.affiliation: Institute for Biomedical Technologies, National Research Council, Segrate, MI, Italy.
authors.forename: Luciano
authors.initials: L
authors.lastname: Milanesi
authors.affiliation: Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Weisz
authors.affiliation: Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy.|Genomix4Life, University of Salerno, Baronissi, SA, Italy.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Giurato
mesh_terms: D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D006816:Huntington Disease / Q000378:metabolism; D035683:MicroRNAs; D034741:RNA, Small Interfering; D058727:RNA, Small Untranslated; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering; D058727:RNA, Small Untranslated