PriSM

PriSM designs degenerate primers for amplification and sequencing of short viral genomes to preserve sample population diversity relevant to studies of viral evolution, transmission, and drug resistance.

Key Features:

• Algorithmic efficiency: PriSM uses computational algorithms to select and match degenerate primer pairs, enabling design of panels containing hundreds of primer pairs within hours.
• Rapid in silico optimization: The tool supports fast in silico optimization of candidate primers for sequencing-oriented workflows.
• Validation and application: PriSM has been applied to construct an amplification primer panel for human immunodeficiency virus (HIV) Clade B, demonstrating its design approach in a virology use case.

Scientific Applications:

• High-throughput amplification and sequencing panel design: Enables scalable generation of large primer panels for amplification and sequencing of short viral genomes.
• Capture of genetic diversity for evolutionary and epidemiological studies: Supports degenerate primer designs that preserve within-host and between-host genetic variability for studies of viral evolution, transmission, and drug resistance.
• HIV primer panel construction: Applicable to construction of amplification primer panels for HIV Clade B as a practical validation example.

Methodology:

PriSM automates degenerate primer design using computational algorithms to replace manual primer selection, accelerating primer panel generation while improving reproducibility and consistency.