LRIscan

LRIscan predicts long-range RNA-RNA interactions (LRIs) across complete viral genomes by identifying evolutionarily conserved interaction sites relevant to viral replication.

Key Features:

• Multiple Genome Alignment-Based Prediction: Utilizes multiple viral genome alignments to identify evolutionarily conserved LRIs.
• Validation of Known Interactions: Successfully validated 14 out of 16 experimentally known and evolutionarily conserved LRIs across Hepatitis C Virus (HCV), Tombusviruses, Flaviviruses, and Human Immunodeficiency Virus-1 (HIV-1).
• Discovery of New Interactions: Identifies novel candidate LRIs characterized by compensatory mutations that are conserved across the analyzed viral sequences.
• Reactivity Plots for Interaction Hot Spots: Generates reactivity plots that highlight predicted LRI hot spots within viral RNA genomes.
• Implementation: Implemented in Ruby/C++ and provided to run on Linux and Windows platforms.

Scientific Applications:

• Genome-wide LRI screening: Enables comprehensive screening of full viral genomes to identify conserved LRIs relevant to viral replication and genome architecture.
• Comparative virology: Facilitates comparative analysis of conserved LRIs across virus families such as HCV, Tombusviruses, Flaviviruses, and HIV-1.
• Experimental prioritization: Assists in prioritizing regions for experimental validation by combining conservation, compensatory mutation evidence, and reactivity plot hotspots.

Methodology:

Uses multiple genome alignments to predict conserved LRIs, detects compensatory mutations, validates predictions against experimentally known LRIs, and produces reactivity plots; implemented in Ruby/C++ for Linux and Windows.