MISIS

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.[1]

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.[2]

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