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Table 1 Subset of 18 most informative miRNA hairpin descriptors

From: In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity

Descriptor Explanation Bound. a Typeb Discriminative powerc Kd
bulgeRatio ratio asymmetrical bulges vs. stem length str 1.45 0.416
dP adjusted base pairing propensity (dP) str 2.28 0.417
largest bulge longest bulge in stem (nt) str 1.74 0.343
longest match-stretch longest match-stretch in stem (nt) str 1.20 0.336
Looplength central loop length (nt) str 1.17 (u) 0.191
max match count matches in 24 nt str 2.75 0.477
MFEahl index [39] MFEahl corrected for GC- Content str 4.75 0.706
Q [37, 39] Normalized Shannon entropy (Q) str 3.01 0.844
stem length stem length ↑↓ str 1.29 (l) 0.404
GAsurplusCU surplus of GA over CU in sequence ↑↓ seq 1.12 (u) 1.05 (l) 0.195
GsurplusC surplus of G over C in sequence seq 1.12 0.995
polyA longest poly-A stretch (nt) seq 1.58 0.834
polyNucHairpin longest mono-nucleotide stretch (nt) in the hairpin seq 1.64 0.846
polyU longest poly-U stretch (nt) seq 1.53 0.540
SCS-di Di-nucleotide Sequence Complexity (-) seq 1.77 0.557
SCS-mono Mono-nucleotide Sequence Complexity (-) seq 1.60 0.317
GU-match contribution ratio of GU-matches vs. all matches mix 1.28 0.173
MFEahl (dG) [37, 39] MFE Adjusted for hairpin length mix 13.33 0.742
  1. A detailed explanation of all 40 descriptors is given in the additional information [see Additional files 1 and 2].
  2. a Boundary; indication of extreme tail of descriptor distribution that was transformed into S < 1 fraction. Symbols denote: ↓ lower tail; ↑ upper tail, and; ↓↑ both tails.
  3. b Type; descriptor based on structural (str), sequence (seq) or both structural and sequence (mix) properties of the hairpin.
  4. c Discriminative power; expressed at 95% sensitivity, measured on the taxonomic set Metazoa (3,902 miRNA hairpins, positives) and genomic hairpins in C. elegans (3,526,115 hairpins, negatives). * Discriminative power of descriptor 'Z' was measured on 25,599 identified hairpins in four viruses.
  5. d K; highest Cohen's kappa coefficient [41] with another descriptor, measured on the taxonomic set Metazoa with S < 1 cut-off of 95%.