Table 1 Parameters calculated on FindMiRNA predictions and thresholds adopted for selection of predictions
Parameter name | Parameter description | Parameter cutoff | |
|---|---|---|---|
mirna_exon | selected_predictions | ||
Position in precursor | Indicates the miRNA* position (at the precursor 5' or 3' end) | ||
Strand | Indicates the precursor strand where the mirna* is located (+ or -) | ||
5'U present | Retains only those records for which a U residue is present in the -2, -1, +1 and +2 positions with respect to the 5' nucleotide of the predicted miRNA sequence. | yes | yes |
miRNA % G+C content | G+C percentage in the mature miRNA sequence | ≥ 33 and ≤ 65 | ≥ 33 and ≤ 65 |
Precursor length | Length of the precursor in base pairs | ≥ 45 bp | ≥ 72 bp and ≤ 442 bp |
MFE | Minimum free energy: estimated stability of the miRNA-candidate::target duplex | ≤ -28 | ≤ -28 |
Precursor % G+C content | G+C percentage in the precursor sequence | ≥ 35 and ≤ 66 | |
Precursor homology % | Percentage of homology in the precursor hairpin | > 50 | |
Length normalized MFE (MFEs) | Minimum free energy of the precursor secondary structure normalized according to precursor length | ≤ -0.23 and ≥ -0.66 | |
MFEI | MFEs/% G+C content | ≤ -0.005 and ≥ -0.012 | |
Self containment | Precursor self containment index, as calculated by Selfcontain | ≥ 0.89 | |