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Attention:
Due to technical maintenance some tools might be unavailable. See maintenance information. 
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paRNAss - Manual
Users and friends of paRNAss:
Our recent tool RNAshapes computes exact probabilities of an RNA molecule folding into either one of several alternative shapes. This is precise information on what paRNAss tries to achieve by sampling. Consider using RNAshapes in shape probability mode, for your task! paRNAss is out of service.
Our recent tool RNAshapes computes exact probabilities of an RNA molecule folding into either one of several alternative shapes. This is precise information on what paRNAss tries to achieve by sampling. Consider using RNAshapes in shape probability mode, for your task! paRNAss is out of service.
paRNAss parameters:
- Suboptimality threshold P in kcal/mol gives the energy
range above the mfe to be analysed: typical values 2 - 5.
The bigger P the bigger the number of structures generated (exponential searchspace!). - Searchspace: feasible structures are all plausible structures of the current energy model, whereas canonicals further disallow isolated base pairs and though reduce the searchspace.
- Temperature T: normally 37
- Maximal number N of structures. If the number of structures generated under the settings of P and T exceeds N, N of tthem are chosen equally distributed. Be careful with this option: Choosing too little number might result in loss of relevant structures, whereas large N lead to increased computation time (paRNAss behaves quadratic on the number of structures because of the pairwise distance calculation. Especially the usage of the Tree Alignment Distance is very time consuming.
- Tree Alignment Distance: This Distance measure is calculated by RNAforester.
Documentation:
- A paper describing paRNAss can be found here.
- A detailed documentation of paRNAss is available here (german version only).
- A new approach to analyzing RNA foldings is described in this draft paper (about 40 pages).
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