IGEM:Melbourne/2008/BCRiboswitch/Online programs
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1.http://frontend.bioinfo.rpi.edu/applications/mfold/
This was what Isaacs et al. used. It can be used to simulate the loop structures of RNA.
Zuker, M (2003). Mfold web server for nucleic acid folding and hybridisation prediction. Nucleic Acids Research vol. 31 (No. 13).
2.http://riboswitch.bioapps.biozentrum.uni-wuerzburg.de/server.html
You can enter your mRNA sequence (I think) into this and look for already existing riboswitches.
Bengert, P & Dandekar, T (2004). Riboswitch finder—a tool for identification of riboswitch RNAs. Nucleic Acids Research 32 --explains how to use the above program
