dna - Primer Dimer / Hairpin Algorithms

It is important visualize more faces to design primer or oligo and PCR experiments:

- calculate thermodynamic parameters of DNA Hybridization (Oligo/Template)

• compute hairpin-loop, dimer, bases penality and melting temperature about primer or pair primer




• calculate statistics about melting temperature with the change in composition and mix PCR concentration

with google you could find more tools but you must choose a tool of a sequencing team.
almost all tools use mfold algorithm, it's simple and effective:

M. Zuker, D. H. Mathews & D. H. Turner. Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide In A Biochemistry and Biotechnology, 11-43, J. Barciszewski and B. F. C. Clark, eds. , NATO ASI Series, Kluwer Academic Publishers, Dordrecht, NL, 1999.

I worked in a sequencing team and there was a programmer. he developed a fantastic tools. he is a little english, but he could support you: http://promix.cribi.unipd.it/cgi-bin/promix/melting/melting_main.exe