MFEprimer-2.0

MFEprimer-2.0 predicts and evaluates PCR primer binding sites, specificity, and thermodynamic stability against genomic and transcriptomic databases.

Key Features:

• K-mer Index Algorithm: Uses a k-mer index algorithm to accelerate searches for potential primer binding sites against sequence databases.
• Thermodynamic Evaluation: Calculates primer–template thermodynamic stability and melting temperature (Tm) to assess binding under PCR conditions.
• Comprehensive Reporting: Reports sequence specificity, predicted melting temperature (Tm), and amplicon sizes for specific and non-specific products.
• Support for Degenerate and Multiple Primers: Handles degenerate primers and multiple PCR primer sets within a single analysis.
• Comprehensive Databases: Searches extensive genomic and transcriptomic databases and can incorporate custom databases.

Scientific Applications:

• Primer Specificity Assessment: Evaluates primer specificity and predicts off-target amplification against genomic and transcriptomic datasets.
• PCR Assay Optimization: Informs primer selection by providing Tm and predicted amplicon sizes to optimize PCR conditions.
• Design with Degenerate/Multiple Primers: Enables evaluation of degenerate and multiple primer sets for applications requiring variable target sequences.

Methodology:

MFEprimer-2.0 applies a k-mer index algorithm to locate candidate primer binding sites and performs thermodynamic calculations to evaluate primer–template stability and melting temperature.