title: MISIS: a bioinformatics tool to view and analyze maps of small RNAs derived from viruses and genomic loci generating multiple small RNAs.
abstract: In eukaryotes, diverse small RNA (sRNA) populations including miRNAs, siRNAs and piRNAs regulate gene expression and repress transposons, transgenes and viruses. Functional sRNAs are associated with effector proteins based on their size and nucleotide composition. The sRNA populations are currently analyzed by deep sequencing that generates millions of reads which are then mapped to a reference sequence or database. Here we developed a tool called MISIS to view and analyze sRNA maps of genomic loci and viruses which spawn multiple sRNAs. MISIS displays sRNA reads as a histogram where the x-axis indicates positions of the 5'- or 3'-terminal nucleotide of sense and antisense sRNAs, respectively, along a given reference sequence or its selected region and the y-axis the number of reads starting (for sense sRNA) or ending (for antisense sRNA) at each position. Size-classes of sRNAs can be visualized and compared separately or in combination. Thus, MISIS gives an overview of sRNA distribution along the reference sequence as well as detailed information on single sRNA species of different size-classes and abundances. MISIS reads standard BAM/SAM files outputted by mapping tools and generates table files containing counts of sRNA reads at each position of the reference sequence forward and reverse strand and for each of the chosen size-classes of sRNAs. These table files can be used by other tools such as Excel for further quantitative analysis and visualization. MISIS is a Java standalone program. It is freely available along with the source code at the following website: http://www.fasteris.com/apps.
authors.affiliation: Zürich-Basel Plant Science Center, University of Basel, Department of Environmental Sciences, Botany, Hebelstrasse 1, 4056 Basel, Switzerland; Fasteris SA, Ch. du Pont-du-Centenaire 109, 1228 Plan-les-Ouates, Switzerland.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Seguin
authors.forename: Patricia
authors.initials: P
authors.lastname: Otten
authors.forename: Loïc
authors.initials: L
authors.lastname: Baerlocher
authors.forename: Laurent
authors.initials: L
authors.lastname: Farinelli
authors.forename: Mikhail M
authors.initials: MM
authors.lastname: Pooggin
mesh_terms: D019295:Computational Biology / Q000379:methods*; D056890:Eukaryota; D056426:Genetic Loci; D058727:RNA, Small Untranslated / Q000235:genetics*; D014780:Viruses / Q000235:genetics*
chemical_list: D058727:RNA, Small Untranslated
keywords: Bioinformatics tool; Plant virus; Virus; miRNA; piRNA; siRNA