title: MISIS-2: A bioinformatics tool for in-depth analysis of small RNAs and representation of consensus master genome in viral quasispecies.
abstract: In most eukaryotes, small RNA (sRNA) molecules such as miRNAs, siRNAs and piRNAs regulate gene expression and repress transposons and viruses. AGO/PIWI family proteins sort functional sRNAs based on size, 5'-nucleotide and other sequence features. In plants and some animals, viral sRNAs are extremely diverse and cover the entire viral genome sequences, which allows for de novo reconstruction of a complete viral genome by deep sequencing and bioinformatics analysis of viral sRNAs. Previously, we have developed a tool MISIS to view and analyze sRNA maps of viruses and cellular genome regions which spawn multiple sRNAs. Here we describe a new release of MISIS, MISIS-2, which enables to determine and visualize a consensus sequence and count sRNAs of any chosen sizes and 5'-terminal nucleotide identities. Furthermore we demonstrate the utility of MISIS-2 for identification of single nucleotide polymorphisms (SNPs) at each position of a reference sequence and reconstruction of a consensus master genome in evolving viral quasispecies. MISIS-2 is a Java standalone program. It is freely available along with the source code at the website http://www.fasteris.com/apps.
authors.affiliation: 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.affiliation: Fasteris SA, Ch. du Pont-du-Centenaire 109, 1228 Plan-les-Ouates, Switzerland.
authors.forename: Patricia
authors.initials: P
authors.lastname: Otten
authors.affiliation: Fasteris SA, Ch. du Pont-du-Centenaire 109, 1228 Plan-les-Ouates, Switzerland.
authors.forename: Loïc
authors.initials: L
authors.lastname: Baerlocher
authors.affiliation: Fasteris SA, Ch. du Pont-du-Centenaire 109, 1228 Plan-les-Ouates, Switzerland.
authors.forename: Laurent
authors.initials: L
authors.lastname: Farinelli
authors.affiliation: University of Basel, Department of Environmental Sciences, Botany, Hebelstrasse 1, 4056 Basel, Switzerland. Electronic address: Mikhail.Pooggin@unibas.ch.
authors.forename: Mikhail M
authors.initials: MM
authors.lastname: Pooggin
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016679:Genome, Viral; D010942:Plant Viruses / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D058727:RNA, Small Untranslated; D012367:RNA, Viral; D012984:Software
chemical_list: D058727:RNA, Small Untranslated; D012367:RNA, Viral
keywords: Bioinformatics tool; Consensus sequence; Single nucleotide polymorphism; Small RNA; Viral quasispecies; siRNA