Table 2.
Feature descriptors calculated by iLearnPlus for DNA and RNA sequences
| Descriptor group | Descriptor (abbreviation) | Sequence type | Reference |
|---|---|---|---|
| Nucleic acid composition | Nucleic acid composition (NAC) | DNA/RNA | (15) |
| Enhanced nucleic acid composition (ENAC) | DNA/RNA | (15) | |
| k-spaced nucleic acid pairs (CKSNAP) | DNA/RNA | (15) | |
| Basic kmer (Kmer) | DNA/RNA | (71) | |
| Reverse compliment kmer (RCKmer) | DNA | (72,73) | |
| Accumulated nucleotide frequency (ANF) | DNA/RNA | (74) | |
| Nucleotide chemical property (NCP) | DNA/RNA | (74) | |
| The occurrence of kmers, allowing at most m mismatches (Mismatch) | DNA/RNA | (20) | |
| The occurrences of kmers, allowing non-contiguous matches (Subsequence) | DNA/RNA | (20) | |
| Adaptive skip dinucleotide composition (ASDC) | DNA/RNA | (47) | |
| Local position-specific dinucleotide frequency (LPDF) | DNA/RNA | (75) | |
| The Z curve parameters for frequencies of phase-specific mononucleotides (Z_curve_9bit) | DNA/RNA | (76) | |
| The Z curve parameters for frequencies of phase-independent dinucleotides (Z_curve_12bit) | DNA/RNA | (76) | |
| The Z curve parameters for frequencies of phase-specific dinucleotides (Z_curve_36bit) | DNA/RNA | (76) | |
| The Z curve parameters for frequencies of phase-independent trinucleotides (Z_curve_48bit) | DNA/RNA | (76) | |
| The Z curve parameters for frequencies of phase-specific trinucleotides (Z_curve_144bit) | DNA/RNA | (76) | |
| Residue composition | Binary (binary) | DNA/RNA | (62,63) |
| Dinucleotide binary encoding (DBE) | DNA/RNA | (75) | |
| Position-specific of two nucleotides (PS2) | DNA/RNA | (20,77) | |
| Position-specific of three nucleotides (PS3) | DNA/RNA | (20,77) | |
| Position-specific of four nucleotides (PS4) | DNA/RNA | (20,77) | |
| Position-specific tendencies of trinucleotides | Position-specific trinucleotide propensity based on single-strand (PSTNPss) | DNA/RNA | (78,79) |
| Position-specific trinucleotide propensity based on double-strand (PSTNPds) | DNA | (78,79) | |
| Electron-ion interaction pseudopotentials | Electron-ion interaction pseudopotentials value (EIIP) | DNA | (80,81) |
| Electron-ion interaction pseudopotentials of trinucleotide (PseEIIP) | DNA | (80,81) | |
| Autocorrelation and cross-covariance | Dinucleotide-based auto covariance (DAC) | DNA/RNA | (53–55) |
| Dinucleotide-based cross covariance (DCC) | DNA/RNA | (53–55) | |
| Dinucleotide-based auto-cross covariance (DACC) | DNA/RNA | (53–55) | |
| Trinucleotide-based auto covariance (TAC) | DNA | (53) | |
| Trinucleotide-based cross covariance (TCC) | DNA | (53) | |
| Trinucleotide-based auto-cross covariance (TACC) | DNA | (53) | |
| Moran (Moran) | DNA/RNA | (49,50) | |
| Geary (Geary) | DNA/RNA | (51) | |
| Normalized Moreau-Broto (NMBroto) | DNA/RNA | (52) | |
| Physicochemical property | Dinucleotide physicochemical properties (DPCP type 1 and type 2) | DNA/RNA | (82) |
| Trinucleotide physicochemical properties (TPCP type 1 and type 2) | DNA | (82) | |
| Mutual information | Multivariate mutual information (MMI) | DNA/RNA | (83) |
| Similarity-based descriptor | K-nearest neighbor (KNN) | DNA/RNA | (83) |
| Pseudo nucleic acid composition | Pseudo dinucleotide composition (PseDNC) | DNA/RNA | (53,84) |
| Pseudo k-tupler composition (PseKNC) | DNA/RNA | (53,84) | |
| Parallel correlation pseudo dinucleotide composition (PCPseDNC) | DNA/RNA | (53,84) | |
| Parallel correlation pseudo trinucleotide composition (PCPseTNC) | DNA | (53,84) | |
| Series correlation pseudo dinucleotide composition (SCPseDNC) | DNA/RNA | (53,84) | |
| Series correlation pseudo trinucleotide composition (SCPseTNC) | DNA | (53,84) |