I have a file with many predicted miRNAs. I need to perform a randomization test to identify which of these miRNAs are highly probable. This test is to randomize each predicted miRNA 1000 times and calculate each randomized sequence's MFE value (this can be easily done by RNAfold). My current problem is how to generate 1000 radomized sequences for each miRNA? I make an example below.
Predicted miRNAs file
>miR1 augcgugaccguaugcuac >miR2 uuuggugcguagucguacg ............ >miR100 auaugagucguacguacgu
Radomized sequences file
>miR1_1 ugcggaccguaugcuacau >miR1_2 ugcggaccuugcuacauga ........... >miR1_1000 ugcggaccguaugcuacua ............. ............ >miR100_1000 auaugagucgacguacu
Could anyone being familar with perl help to solve this problem? For the next steps including calculating MFE etc, I can do them myself. But I believe someone who know well RNAfold and miRNA prediction can produce a pipline for this work. I attached a Nucleic Acid Research reference link here http://nar.oxfordjournals.org/content/37/suppl_1/D111.full . In the method section, when searing RNAFOLD, you can find the authors' method. THANK YOU in advance!