Concentration plot does not plot the AA concentration correctly

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rimal
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Joined: 08/22/2014

In homodimer simulation on the web server, the concentration plot is weird: the AA concentration is obviously multiplied by two (starts at the same level as the A concentraion stops). Note that almost no Af is present in my oligos. The melting temperature Tm(conc) does not appear where the two lines cross each other (i.e., half of the strands are hybridized). When I downloaded the data, the crossing occurs correctly at TmConc.
So, my observation is: TmConc value is correct, but the plot of AA concentration is not.

prathameshshimpi03
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Joined: 05/17/2015
Thanks so much

Thanks for sharing with us my problem is solve now i like your post best data recovery software

rimal
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Joined: 08/22/2014
Mole fraction

Right, I see - it displays the mole fraction, not the concentrations themselves (which are stored in the data file A-A.conc). Now it is clear.
But still - it might be more illustrative to put the concentration values in the concentration plot instead of the mole fractions; then, the lines should cross each other precisely at TmConc.

zukerm
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Joined: 11/12/2010
We decided to use mole

We decided to use mole fractions so that the top of the plot would always be 1 and the different curves would sum to 1. I ran a simple contrived example of a self-complementary DNA that is 100% hybridized at low temperature and completely melted at high temperature. I used the "advanced form" where I excluded folding. When the lines cross, the mole fractions are equal, but 2/3 of the DNA is double stranded. At TmConc, half of the strands are single-stranded by definition, but the mole fraction of dimers is 1/3. I see no problem. In general, two sequences are used. The concentration of species A can be different from the concentration of species B. All molecular species can be present at a particular temperature. Many lines are crossing. The notion that TmConc should correspond to a crossing of lines becomes meaningless in such a case. At least we provide a file containing actual concentrations.