NetPrimer combines the latest primer design algorithms with a web-based interface allowing the user to analyze primers over the Internet. All primers are analyzed for melting temperature using the nearest neighbor thermodynamic theory to ensure accurate Tm prediction. Primers are analyzed for all secondary structures including hairpins, self-dimers, and cross-dimers in primer pairs. This ensures the availability of the primer for the reaction as well as minimizing the formation of primer dimer. The program eases quantitation of primers by calculating primer molecular weight and optical activity.? To facilitate the selection of an optimal primer, each primer is given a rating based on the stability of its secondary structures. A comprehensive analysis report can be printed for individual primers or primer pairs.
Primer properties: Tm , molecular weight, GC%, optical activity (both in nmol/A260 & 礸/A260), DG, 3' end stability, DH, DS, and 5' end DG.
Secondary structures:Hairpins, dimers, cross dimers, palindromes, repeats and runs.
Primer rating: Quantitative prediction of the efficiency of a primer.
Comprehensive report:Prints complete primer analysis for an individual primer or primer pair
Primer pairs:Analyze individual primers or primer pairs.
Comprehensive help:Details all the formulas and references used in primer analysis algorithm.