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paRNAss - Welcome

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 will soon go out of service.

RNAmovie of the E.coli trp-Attenuator changing between its two possible conformations.

paRNAss

Prediction of Alternating RNA Secondary Structures

There are various cases where the biological function of an RNA molecule involves a reversible change of conformation. paRNAss is a software approach to the prediction of such structural switching in RNA. It is based on a three hypotheses about the secondary structure space of a switching RNA molecule, which can be evaluated by RNA folding and structure comparison. In the positive case, the predicted structures must be verified experimentally. Additionally, we give an animated visualization of an energetically favourable transition between the predicted structures.

Authors: Bjoern Voss, Int. NRW Graduate School in Bioinformatics and Genome Research, Marc Rehmsmeier, Dirk Haase

E-Mail: bvoss(at)techfak.uni-bielefeld.de

(Simply replace the (at) with the usual @ to get the correct email adress. Please help to avoid spam !)

If you use paRNAss in your own research, please cite:
Prediction and visualization of structural switches in RNA, R. Giegerich, D. Haase and M. Rehmsmeier, Pac. Symp. Biocomput., Pages: 126-137, 1999