Problem with ct-prob

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JJ
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Joined: 06/24/2013

I am using ct-prob Ver 3.8. I tried to calculate the propabilities of 100 foldings of an ssDNA strand. The problem is, that if the last nucleotide (3'-end) of the folding is paired to another one, ct-prob does not calculate a probability for that pairing (the line is missing in the plot-file). This leads to a probability of zero after plot2ann for the two paired nucleotides, since they are paired in the ct-file and eventually to a black color.

zukerm
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Joined: 11/12/2010
I tested ct-prob myself and

I tested ct-prob myself and found exactly the same problem. I regard this as a major bug and I apologize for it. I found that if I add an extra nucleotide at both ends (I use "N"), then the application works properly.

I regret that it took so long for this problem to come to my attention. Thank you for reporting it.