calculates oligo melting temperature (Tm) and GC content. This tool is using small application called oligotm from Primer3 package.
Calculations of the melting temperature and salt correction are based on the formulas published in:
- Breslauer KJ, Frank R, Blöcker H and Marky LA. (1986) Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci., 83, 4746-50.
- Rychlik W, Spencer WJ and Rhoads RE. (1990) Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acids Res., 118, 6409-12.
- SantaLucia JR. (1998). A unified view of polymer, dumbbell and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci., 95, 1460-65.
- Schildkraut, C, and Lifson, S. (1965) Dependence of the melting temperature of DNA on salt concentration. Biopolymers, 3, 195-208.
- Owczarzy R, You Y, Moreira BG, Manthey JA, Huang L, Behlke MA and Walder JA. (2004) Effects of Sodium Ions on DNA Duplex Oligomers: Improved Predictions of Melting Temperatures. Biochemistry, 43, 3537-54.
- Owczarzy R, Moreira BG, You Y, Behlke MA and Walder JA. (2008) Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations. Biochemistry, 47, 5336-53.
Here is a list of updates and bugfixes: update.txt
Here is a correct input file: sample.txt
For further information please contact: .
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