I need a DNA library pool to be generated using in-silico approach and have to analyze which will be more stable in conformation. In a pool of sequences, it is highly tedious to analyze structure prediction for each sequence manually. Is there any program or software available to predict structures and their stability for all DNA sequences at a time? I have come to know that Vienna RNA package can compute nearly 100 samples to the maximum at a time. Can anyone tell how to run 100 samples at a time for structure prediction?
Pl consult the article
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2910066/
Sir, I have tried to generate pools of sequences using RAG pools web server. How long will it take to generate pool? Because I have send specifications to generate a pool a day before. But still result has not been sent to me.
ํYou may use standalone version of VIenna package combination with for loop over a list of sequences files.
RNAfold (from the standalone version of the Vienna package; see https://www.tbi.univie.ac.at/RNA/) is able to handle files containing many sequences; see its manual for examples.
@Gerhard Steger
when I try to use RNAfold web server to predict for multiple sequences at a time it was actually merging all sequences in a single line and then calculating energy rather than predicting for each sequence.
The web server accepts only single sequences, but the stand-alone version accepts a file containing many sequences, as already mentioned.
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