Rna prediction software

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The Predict a Secondary Structure server combines four separate prediction and analysis algorithms: calculating a partition function, predicting a minimum free energy MFE structure, finding structures with maximum expected accuracy, and pseudoknot prediction.

This server takes a sequence, either RNA or DNA, and creates a highly probable, probability annotated group of secondary structures, starting with the lowest free energy structure and including others with varied probabilities of correctness.

Other structures are included because the minimum free energy structure may not be the correct one. This SHAPE structure group is distinct from the probability annotated structure group, and is not probability annotated itself. To get more information on the meaning of the options click the symbols. You can test the server using this sample sequence. Show constraint folding.

Show advanced options. Or upload a file with the reactivities:. Notification via e-mail upon completion of the job optional :. Paste or type your sequence here: [clear].

It predicts the secondary structure of RNAs with a limit to 75oo nucleotides for partition function prediction and 10, nucleotides for minimum free energy predictions. The minimum free energy structure prediction is based on a loop-based energy model and a dynamic programming algorithm. The energy minimized RNA structure is predicted according to the given energy parameter set and temperature [2]. It also provides additional features including biomolecular structure prediction, base-pairing probabilities, and equilibrium binding affinities prediction [3].

The latest version of RNAstructure Version6. It is completely based on machine learning. But the reported prediction accuracy is high on the tested data [4].

The source code can be downloaded from GitHub. It offers several online webservers for secondary structure prediction and RNA design.