NetPrimer is a gratis web-based tool used for analysing primers used in PCR to amplify a DNA sequence. The software predicts the melting temperature of the primers using the nearest neighbor thermodynamic algorithm. The accurate prediction of the melting temperature (Tm) is one of the most important factors that governs the success of a PCR reaction. NetPrimer also analyzes the thermodynamically important secondary structures such as hairpins, self and cross dimers, runs and repeats. These structures significantly affect the primer efficiency and therefore the success of a PCR reaction.