Predicting effects of chemical modification on ssDNA folding

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Subho
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Joined: 05/12/2011

I am looking for a software that can predict secondary structure adopted by ssDNA, and the effects of chemical modifications of some bases (e.g. CpG methylation) on their stability. I have explored the mfold and other fold prediction software, but could not to find one that can address this issue. It is an old problem and someone must have thought about it. Can you please guide me to the right direction?