Temperature calculation

The primer melting temperature is calculated using a nearest-neighbors approach similar to the one used by MELTING [Novere, 2001]. However, the Primer Creator uses the nearest-neighbor model and interaction parameters given in [SantaLucia et al., 2000], which give rise to some differences in the melting temperatures calculated by the two tools. Temperatures are corrected for salt concentration and dangling-end parameters are used [Bommarito et al., 2000]. Nucleotide mismatches are handled using the parameters defined in [Allawi and SantaLucia, 1997,Allawi and SantaLucia, 1998a,Allawi and SantaLucia, 1998c,Allawi and SantaLucia, 1998b,Peyret et al., 1999]. If the concentration of DMSO, dNTP or Magnesium is greater than zero, the temperature correction defined in [von Ahsen et al., 2001] is used.