MiRfold searches for a good miRNA-like folding in the sequence surrounding a putative miRNA. It was optimized on plant miRNAs.
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B. Billoud, R. De Paepe, D. Baulcombe and M. Boccara,
“Identification of new small non-coding RNAs from tobacco and Arabidopsis”
Biochimie 2005, 87 (9-10):905-910.