A randomization test for sequence secondary structure.
This is RandFold version 2. The software computes the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from a distribution of MFE computed with random sequences.
RandFold was developed by Eric Bonnet at the Bioinformatics & Evolutionary Genomics group, Universiteit Gent in Belgium. A web page referencing the research may be found at bioinformatics.psb.ugent.be.
UsageBefore running RandFold, you need to load the appropriate module, as in the example below:
module load randfold randfold <method> <file name> <number of randomizations>
-s simple mononucleotide shuffling
-d dinucleotide shuffling
-m markov chain 1 shuffling
randfold -d let7.tfa 999
<sequence name> tab <mfe> tab <probability>Example:
cel-let-7 -42.90 0.001000
For more information, see the paper published in Bioinformatics:
Bonnet E., Wuyts J., Rouze P., Van de Peer Y.
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences.
Bioinformatics. 2004 Nov 22;20(17):2911-7.
A large collection of protein sequence databases is in /fdb/fastadb/.
Fasta-format databases and update status.