Hi I was wondering if there is any online software to check the Tm specifically for PCR product?
Type primer designing or Tm finder in Google, you will get tons of tool.
Hi
Try Oligo Analyzer. Please find the link below, which will take you to the oligo analyzer tool.
http://eu.idtdna.com/analyzer/Applications/OligoAnalyzer/
Good Luck :)
Hi,
Oligocalc is a good analyzer. It gives you TM of oligo as well as potential secondary structure.
http://www.basic.northwestern.edu/biotools/OligoCalc.html
I advise you all this one too, http://biologylabs.utah.edu/jorgensen/wayned/ape/
dear there is sequence manipulation suite available online software which has various applications one of them is primer stats in which you will not only know Tm but various other parameters of your primer like hair pin chances, GC content, self annealing chances, etc
I am trying to find a online software which calculates TM of the PCR product NOT of the primer/oligos.
http://www.ncbi.nlm.nih.gov/pubmed/1718662
Hi, as my modest knowledge, there is not a software to calculate that, but it's very easy to do it by your self, just youhave to know some basics about PCR, primers, so i can give you some simple rules to apply to find what you need to know:
You must define the Tm (melting temp = temperature at which
50% of the DNA is in the single-stranded form)
Tm = 81.5 ° C + + 16,6logM 0.41 (% G +% C) - 500 / l - 0,6f -1,5m
M: molar concentration of monovalent ions
l: length of the primer (base)
f: percentage of formamide
m: percentage of mismatch
Tm = 2 ° C x [A + T] + 4 ° C x [G + C] (primers 14 to 24 bases)
Tm relatively high and close (diff
I agree with BOUALLEGUI or same software which you use to calculate the Tm of the primer or oligos. Same thing you can use for the identification of the Tm of the PCR product.
You can try any of the above mentioned by RKP. I used to prefer most.
http://tmcalculator.neb.com/#!/
Hi Preetam,
May I ask you, why you are interested in Tm of the PCR product? and I am there are some nucleic acid thermodynamic tools available for your purpose. Just remember that it is only an average measure, it can be influenced by various factors such as the concentration of salts around, DNA itself etc.
Hi Younes, you wrote :
" You must define the Tm (melting temp = temperature at which
50% of the DNA is in the single-stranded form)
Tm = 81.5 ° C + + 16,6logM 0.41 (% G +% C) - 500 / l - 0,6f -1,5m
M: molar concentration of monovalent ions
l: length of the primer (base)
f: percentage of formamide
m: percentage of mismatch
Tm = 2 ° C x [A + T] + 4 ° C x [G + C] (primers 14 to 24 bases)
Tm relatively high and close (diff
@ Dear Davide
Normally, you will find all the concentrations of the different ingredients on the technical sheet that you received with your primers, or also some of those information are written on the tube (it depend on the suppliers, some don't include everything on the tubes),
You're welcome,
All the best,
Younes,
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