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.

Usage

/usr/local/randfold-2.0/bin/randfold <method> <file name> <number of randomizations>

Methods available:
-s  simple mononucleotide shuffling
-d  dinucleotide shuffling
-m  markov chain 1 shuffling

Example:

randfold -d let7.tfa 999

Output:

<sequence name> tab <mfe> tab <probability>

Example:

cel-let-7       -42.90  0.001000

More information

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.
PMID: 15217813

A large collection of protein sequence databases is in /fdb/fastadb/.
Fasta-format databases and update status.