How does Jellyfish calculate the melting temperature of oligonucleotides?
Jellyfish uses three different methods to calculate oligonucleotide melting temperatures. The first method, which is a good approximation for oligonucleotides that are 20 bases or less, is the Wallace calculation (1): Tm = 2oC(A+T) + 4oC(G+C) = Tm (basic)> The second method that Jellyfish uses to calculate melting temperatures is the GC Content method, also called the long probe method (2). This approximation takes into account the length of the oligonucleotide and salt concentration and is suggested for Tm estimations of oligonucleotides longer than 40 bases. > Tm = 81.5 + 0.41(%GC) + 16.6log[M] – 600/L = Tm (GC content) The third melting temperature calculation is the thermodynamic-based nearest neighbor method described in Rychlik et al. (3) and Breslauer et al(4). This most accurate method accounts for the effects of base stacking, salt concentration, and oligonucleotide concentration and is expressed with the following equation: Tm = (dH / (dS + Rln[c/4])) – 273.15 + 16.6log[M] =
