Tuesday, September 6, 2011

Excel Hacks: Calculating Oligo Temperature with the Wallace Rule

Calculating oligonucleotide melting temperatures using the Wallace-Itakura formula (2*(number of A's and T's) + 4*(number of G's and C's)) in Excel is a piece of cake. I rarely use it myself as I typically use nearest neighbor with SantaLucia thermodynamic parameters for oligo design, but on occasion it does come up. Assuming your oligo sequence is in A1, this formula will calculate the Wallace TM:
The formula counts the numbers of A's and T's by making a new oligo sequence with A's and T's removed. It then compares the length of the original oligo to the new one - the difference is the number of A's and T's. Counting G's and C's is done in the same manner. Any base other than A,C, G or T will be ignored in the calculation.

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