Skip to main content

Table 1 Feature set composition, dimension, literature reference

From: Automatic learning of pre-miRNAs from different species

Feature Feature set
  FS1 FS2 FS3 FS4 FS 5 FS6 FS7 Select
Di-nucleotide frequencies (XY, X,Y{A,C,U,G}) x        
% G+C x x      x  
Maximal length of the amino acid string without stop codons (orf)        x  
Percentage of low complexity regions (dm)        x  
Triplets     x   x   
Stacking triplets (X (((,X{A,C,G,U})        x  
Motifs (s s−substrings)      x    
Minimum free energy of folding (MFE)       x   
Randfold (p)       x   
Normalized MFE (dG) x x x     x x
MFE index 1 (M F E I 1) x x x     x x
MFE index 2 (M F E I 2) x x x     x x
MFE index 3 (M F E I 3) x x      x x
MFE index 4 (M F E I 4) x x      x  
Normalized Ensemble Free Energy (NEFE) x x      x x
Normalized difference (M F EE F E) (Diff) x x      x x
Frequency of the MFE structure (Freq) x        
Normalized base-pairing propensity (dP) x   x      
Normalized Shannon entropy (dQ) x x x     x x
Structural diversity (Diversity) x x      x  
Normalized base-pair distance (dD) x   x      
Average base pairs per stem (Avg_Bp_Stem) x x      x  
Normalized A-U pairs counts (|AU|/L) x x      x  
Normalized G-C pairs counts (|GC|/L) x x      x x
Normalized G-U pairs counts (|GU|/L) x x      x x
Content of A-U pairs per stem (%(AU)/s t e m s) x x      x  
Content of G-C pairs per stem (%(GC)/s t e m s) x x      x  
Content of G-U pairs per stem (%(GU)/s t e m s) x x      x x
Cumulative size of internal loops (loops)        x  
Structure entropy (dS) x x      x x
Normalized structure entropy (d S/L) x x      x x
Structure enthalpy (dH) x        
Normalized structure enthalpy (d H/L) x        
Melting energy of the structure x        
Normalized melting energy of the structure x        
Topological descriptor (dF) x x x     x x
Normalized variants (zG, zP and zQ) x        
Normalized variants (zD) x x      x  
Normalized variants (zF) x        
Dimension 48 21 7 32 1300 34 28 13
Reference [21] [21] [33] [23] [34] [35] [19] [12]