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Descriptors calculated by MathFeature for DNA, RNA, and Protein sequences.
| Descriptor groups | Descriptor | Dimension | Sequence | Example (Study with Application or Theory) |
|---|---|---|---|---|
| Binary | L * 4 | DNA/RNA | Ref 1 - Ref 2 | |
| Z-curve | L * 3 | DNA/RNA | Ref 1 - Ref 2 | |
| Real | L | DNA/RNA | Ref 1 - Ref 2 | |
| Numerical Mapping | Integer | L | DNA/RNA/Protein | Ref 1 - Ref 2 |
| EIIP | L | DNA/RNA/Protein | Ref 1 - Ref 2 | |
| Complex Number | L | DNA/RNA | Ref 1 - Ref 2 | |
| Atomic Number | L | DNA/RNA | Ref 1 - Ref 2 | |
| Chaos Game Representation | L * 2 | DNA/RNA | Ref 1 | |
| Chaos Game | Frequency Chaos Game Representation | L - k + 1 | DNA/RNA | |
| Chaos Game Signal (with Fourier) | 19 | DNA/RNA | Ref 1 | |
| Fourier Transform | Numerical Mapping + Fourier | 19 | DNA/RNA/Protein | Ref 1 |
| Entropy | Shannon | k | DNA/RNA/Protein | Ref 1 |
| Tsallis | k | DNA/RNA/Protein | Ref 1 | |
| Graphs | Complex Networks (with threshold) | 12 * t | DNA/RNA/Protein | Ref 1 - Ref 2 |
| Complex Networks (without threshold - v2) | 27 * k | DNA/RNA/Protein | Ref 1 - Ref 2 | |
| Basic k-mer | 4^k | DNA/RNA | Ref 1 | |
| Customizable k-mer | 4^k | DNA/RNA | ||
| Nucleic acid composition (NAC) | 4 | DNA/RNA | Ref 1 | |
| Di-nucleotide composition (DNC) | 16 | DNA/RNA | Ref 1 | |
| Tri-nucleotide composition (TNC) | 64 | DNA/RNA | Ref 1 | |
| ORF Features or Coding Features | 10 | DNA/RNA | Ref 1 - Ref 2 | |
| Fickett score | 2 | DNA/RNA | Ref 1 | |
| Pseudo K-tuple nucleotide composition | - | DNA/RNA | Ref 1 | |
| Other techniques | Accumulated Nucleotide Frequency-ANF | L | DNA/RNA/Protein | Ref 1 |
| ANF with Fourier | 19 | DNA/RNA/Protein | ||
| Xmer k-Spaced Ymer Composition Frequency (kGap) | 4^X * 4^Y or 20^X * 20^Y | DNA/RNA/Protein | Ref 1 - Ref 2 | |
| Amino acid composition (AAC) | 20 | Protein | Ref 1 | |
| Dipeptide composition (DPC) | 400 | Protein | Ref 1 | |
| Tripeptide composition (TPC) | 8000 | Protein | Ref 1 | |
| Basic k-mer | 20^k | Protein | ||
| Customizable k-mer | 20^k | Protein | ||
| Kmer Frequency Mapping | L - k + 1 | Protein | ||
| Kmer Frequency Mapping with Fourier | 19 | Protein |
To use any descriptor, see our documentation.
Note 1: L = length of the longest sequence.
Note 2: k = frequencies of k-mer.
Note 3: t = threshold: number of subgraphs.
Note 4: The reference column represents some studies that apply the descriptor (Similar approach). Other references are cited in our article.