VIRsiRNAdb

VIRsiRNAdb provides a curated repository of experimentally validated siRNAs and short hairpin RNAs (shRNAs) targeting viral genomes to support RNA interference (RNAi)–based antiviral research.

Key Features:

• Extensive siRNA/shRNA Collection: Contains 1,358 experimentally validated siRNA/shRNA sequences targeting genome regions across 42 human viruses, including influenza virus, hepatitis B virus, human papillomavirus (HPV), and SARS coronavirus.
• Detailed Annotations: Each entry includes siRNA sequence, virus subtype, target genome region, cell type used in experiments, specific target object within the viral genome, type of experimental assay, assay-derived efficacy data, information on potential off-target effects, and alignment with reference viral sequences.
• Alternative Efficacies: Provides alternative efficacy data for over 300 siRNAs derived from different experimental setups.
• Advanced Search and Browsing: Enables retrieval of siRNAs by parameters such as virus type, target region, and cell line used in experiments.
• Data Submission and Integration: Supports user data submission and links entries to external databases to integrate broader reference resources.
• Analytical Tools (siTarAlign): Includes siTarAlign for aligning siRNA sequences with reference viral genomes or user-defined sequences to aid sequence-level validation.

Scientific Applications:

• siRNA selection for therapeutics: Identification and selection of potent viral siRNAs for antiviral therapeutic development.
• siRNA design: Design and validation of novel siRNA-based interventions against diverse human viruses.
• Mechanistic analysis: Comparative analysis of experimental efficacy data to inform understanding of RNAi-mediated antiviral responses.

Methodology:

Database entries were manually curated from experimental assays, and siTarAlign performs sequence alignment of siRNAs to reference viral genomes or user-defined sequences.