Rocket-miR

Rocket-miR predicts human microRNA (miRNA) targets in bacterial and fungal pathogens to identify candidate miRNA-based antimicrobials for antibiotic-resistant infections, including ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species).

Key Features:

• Target Prediction: Predicts targets of human miRNAs in bacterial and fungal genomes to identify potential miRNA–pathogen interactions.
• Pathogen Coverage: Supports analysis across 24 recognized human pathogens associated with diseases such as cystic fibrosis, chronic obstructive pulmonary disease (COPD), urinary tract infections, and pneumonia.
• Extendibility: Provides an extendible codebase for addition of further human pathogens commonly associated with hospital-acquired infections.

Scientific Applications:

• Candidate Discovery: Identification of candidate miRNA-based antimicrobial agents targeting pathogen genes and virulence factors.
• Experimental Prioritization: Prioritization of miRNA–pathogen interactions for experimental validation by microbiologists.
• Targeted Therapeutic Exploration: Exploration of pathogen-specific mechanisms amenable to miRNA-mediated modulation.

Methodology:

Computational prediction of human miRNA targets within bacterial and fungal genomes by analyzing interactions between human miRNAs and pathogenic genes.