I have a DNA sequence and I suspect that it forms a curved structure, however, while I am planning the experiments to test this hypothesis, I would like to do some in-silico prediction to help me design the experiments. I don't have any experience with programming, so I am looking for a tool/sever where I can paste the sequence and get the predicted structures as output.
Thank you
There are certain programs and algorithms that may help you doing so.
http://www.ncbi.nlm.nih.gov/pubmed/?term=RDNAnalyzer%3A+A+tool+for+DNA+secondary+structure+prediction+and+sequence+analysis.
this one of them
there are a number of such tools available that you may try.
Dear Afzal,
You can use these following online free analyzers.
1) https://eu.idtdna.com/UNAFold?
2) https://eu.idtdna.com/calc/analyzer
Hope it helps.
I hold that one cannot, from nucleotide residue sequence alone, predict secondary structure. The problem is indeed the reverse of the Traveling Salesman Problem, or TSP. In TSP, one is given a list of cities and the distances between each pair of cities, and from this, one must find an Hamiltonian path. With PFP (the protein folding problem), one is given the Hamiltonian path (owing to steric hindrance), and from this one must find the distances between all chiral carbons. PFP is at least as hard as is TSP.
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