Journal
JOURNAL OF VIROLOGICAL METHODS
Volume 233, Issue -, Pages 37-40Publisher
ELSEVIER SCIENCE BV
DOI: 10.1016/j.jviromet.2016.03.005
Keywords
Small RNA; siRNA; Viral quasispecies; Consensus sequence; Single nucleotide polymorphism; Bioinformatics tool
Funding
- Swiss National Science Foundation [31003A_143882/1]
- European Cooperation in Science and Technology (COST
- grant SERI) [C09.0176]
- Swiss National Science Foundation (SNF) [31003A_143882] Funding Source: Swiss National Science Foundation (SNF)
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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. (C) 2016 Elsevier B.V. All rights reserved.
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