MISIS

MISIS visualizes and analyzes small RNA (sRNA) maps and reconstructs consensus genomes to support studies of miRNAs, siRNAs, piRNAs, sRNA-mediated gene regulation, transposon repression, and viral quasispecies.

Key Features:

• sRNA Mapping and Analysis: Views detailed maps of sRNAs derived from cellular genomic regions and viruses to display distribution and abundance across loci.
• Consensus Sequence Determination: Determines and visualizes consensus sequences within sRNA populations to identify common sequence motifs.
• sRNA Counting by Size and 5'-Terminal Nucleotide: Counts sRNAs by length and 5'-terminal nucleotide identity to discriminate populations sorted by AGO/PIWI family proteins.
• SNP Identification: Identifies single nucleotide polymorphisms at each position of a reference sequence to characterize variability in viral quasispecies.
• Consensus Master Genome Reconstruction: Reconstructs a consensus master genome from sRNA data, including datasets produced by deep sequencing, to recover viral genomes.

Scientific Applications:

• Virology: Reconstruction of viral genomes from sRNA-derived reads and analysis of viral quasispecies diversity and evolution.
• Genomics: Mapping sRNA populations across genomic loci to study interactions with transposons and genome-wide sRNA distribution.
• RNA Silencing and Gene Regulation: Characterization of miRNAs, siRNAs, and piRNAs and their sorting by AGO/PIWI proteins to investigate regulatory roles.

Methodology:

Implemented as a standalone Java program that performs sRNA mapping and visualization, consensus sequence determination, size and 5'-nucleotide counting, per-position SNP identification, and consensus master genome reconstruction from sRNA deep-sequencing data.