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. 2014 May 2;15:124. doi: 10.1186/1471-2105-15-124

Table 1.

Features used in each feature set

Feature
 Reference
 Feature set
    FS1 FS2 FS3 FS4 FS5 FS6 FS7
Dinucleotide frequencies
 [13]
 x
  
  
  
  
  
  
G+C content
 [13,29]
 x
 x
  
  
  
  
 x
Maximal length of the amino acid string without stop codons
 [20]
  
  
  
  
  
  
 x
Low complexity regions detected in the sequence (%)
 [20,30]
  
  
  
  
  
  
 x
Triplets
 [10]
  
  
  
 x
  
 x
  
Stacking triplets (X(((, X∈{A,C,G,U})
 [10,20]
  
  
  
  
  
  
 x
Motifs (ss−substrings)
 [23]
  
  
  
  
 x
  
  
Minimum free energy of folding (MFE)
 [27,28]
  
  
  
  
  
 x
  
Randfold (p)
 [31]
  
  
  
  
  
 x
  
Normalized MFE (dG)
 [27]
 x
 x
 x
  
  
  
 x
MFE index 1 (MFEI1)
 [29]
 x
 x
 x
  
  
  
 x
MFE index 2 (MFEI2)
 [29]
 x
 x
 x
  
  
  
 x
MFE index 3 (MFEI3)
 [16,27]
 x
 x
  
  
  
  
 x
MFE index 4 (MFEI4)
 [16,27]
 x
 x
  
  
  
  
 x
Normalized essemble free energy (NEFE)
 [16,27]
 x
 x
  
  
  
  
 x
Normalized difference (MFE−EFE) (Diff)
 [16,27]
 x
 x
  
  
  
  
 x
Frequency of the MFE structure (Freq)
 [16,27]
 x
  
  
  
  
  
  
Normalized base-pairing propensity (dP)
 [29,32]
 x
  
 x
  
  
  
  
Normalized Shannon entropy (dQ)
 [29,33]
 x
 x
 x
  
  
  
 x
Structural diversity (Diversity)
 [16,29,33]
 x
 x
  
  
  
  
 x
Normalized base-pair distance (dD)
 [16,29,33]
 x
  
 x
  
  
  
  
Average base pairs per stem (Avg_Bp_Stem)
 [16]
 x
 x
  
  
  
  
 x
Average A-U pairs |A−U|/L
 [16]
 x
 x
  
  
  
  
 x
Average G-C pairs |G−C|/L
 [16]
 x
 x
  
  
  
  
 x
Average G-U pairs |G−U|/L
 [16]
 x
 x
  
  
  
  
 x
Content of A-U pairs per stem %(A−U)/stems
 [16]
 x
 x
  
  
  
  
 x
Content of G-C pairs per stem %(G−C)/stems
 [16]
 x
 x
  
  
  
  
 x
Content of G-U pairs per stem %(G−U)/stems
 [16]
 x
 x
  
  
  
  
 x
Cumulative size of internal loops
 [20]
  
  
  
  
  
  
 x
Structure entropy (dS)
 [16,28,29,33]
 x
 x
  
  
  
  
 x
Normalized structure entropy (dS/L)
 [16,28,29,33]
 x
 x
  
  
  
  
 x
Structure enthalpy (dH)
 [16,28,29,33]
 x
  
  
  
  
  
  
Normalized structure enthalpy (dH/L)
 [16,28,29,33]
 x
  
  
  
  
  
  
Melting energy of the structure
 [16,28,34]
 x
  
  
  
  
  
  
Normalized melting energy of the structure
 [16,28,34]
 x
  
  
  
  
  
  
Topological descriptor (dF)
 [29,35]
 x
 x
 x
  
  
  
 x
Normalized variants (zG, zP and zQ)
 [13,29,36]
 x
  
  
  
  
  
  
Normalized variants (zD)
 [13,29,36]
 x
 x
  
  
  
  
 x
Normalized variants (zF) [13,29,36] x            

Detailed descriptions can be found in the corresponding references.