| Tool . | Modification . | Algorithm . | Feature selection . | Encoding scheme(s) . | Benchmark dataset size (modification sites) . | Dataset quality . | Evaluation strategy . | URL/stand-alone package . | Option of batch prediction . | Adjustment of predictor thresholds . | Window size . | Species . | Reference . |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RAMPred | m1A | SVM | None | NCP ANF | 6366 (H. sapiens) 1064 (M. musculus) 483 (S. cerevisiae) | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/RAMPred | Yes | No | 41 | H. sapiens M. musculus S. cerevisiae | [40] |
| iRNA-3typeA | m1A m6A | SVM | None | NCP ANF | 6366 (H. sapiens; m1A) 1064 (M. musculus; m1A) 1130 (H. sapiens; m6A) 725 (M. musculus; m6A) | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/iRNA-3typeA/ | Yes | No | 41 | H. sapiens M. musculus | [41] |
| iRNA-Methyl | m6A | SVM | None | PseDNC RNA property parameters | 1307 | Non-single-nucleotide resolution | 10-fold cross-validation Jackknife test | http://lin-group.cn/server/iRNA-Methyl | Yes | No | 51 | S. cerevisiae | [42] |
| m6Apred | m6A | SVM | None | NCP ANF | 1307 (832/475) | Non-single-nucleotide resolution | Jackknife test Independent test | http://lin-group.cn/server/m6Apred.php | Yes | All High Medium Low | 21 | S. cerevisiae | [43] |
| M6ATH | m6A | SVM | None | NCP ANF | 394 | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/M6ATH | Yes | No | 25 | A. thaliana | [29] |
| RNA-MethylPred | m6A | SVM | None | BPB DNC KNN score | 1307 | Non-single-nucleotide resolution | Jackknife test | MATLAB package | No | No | 51 | S. cerevisiae | [33] |
| TargetM6A | m6A | SVM | IFS | PSNP PSDP k-mer | 1307 (Met2614) 832 (Train1664) | Non-single-nucleotide resolution | Jackknife test | http://csbio.njust.edu.cn/bioinf/TargetM6A (Not available) | No | No | 51/21 | S. cerevisiae | [32] |
| pRNAm-PC | m6A | SVM | None | PCPM | 1307 | Non-single-nucleotide resolution | Jackknife test | http://www.jci-bioinfo.cn/pRNAm-PC | Yes | No | 51 | S. cerevisiae | [44] |
| RNAMethPre | m6A | SVM | None | binary k-mer Relative position value MFE | 29,457 (H. sapiens) 31,728 (Mouse) | Single- nucleotide resolution | Fivefold cross-validation Independent test | http://bioinfo.tsinghua.edu.cn/RNAMethPre/index.html (Not available) | NA | NA | 101 | H. sapiens M. musculus | [31] |
| AthMethPre | m6A | SVM | None | binary k-mer | 6581 | Non-single-nucleotide resolution | Fivefold cross-validation & Independent test | http://bioinfo.tsinghua.edu.cn/AthMethPre/index.html (Not available) | NA | NA | 101 | A. thaliana | [30] |
| M6A-HPCS | m6A | SVM | None | PCPM PseDNC AC CC | 1307 | Non-single-nucleotide resolution | Jackknife test 10-fold cross-validation | http://csbio.njust.edu.cn/bioinf/M6A-HPCS (Not available) | NA | NA | 51 | S. cerevisiae | [45] |
| SRAMP | m6A | RF | None | binary KNN score spectrum | 55,706 (Full transcript mode) 46,992 (Mature mRNA mode) | Single- nucleotide resolution | Fivefold cross-validation | http://www.cuilab.cn/sramp/ | No | No | 251 | H. sapiens M. musculus | [36] |
| MethyRNA | m6A | SVM | None | NCP ANF | 1130 (H. sapiens) 725 (M. musculus) | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/methyrna | Yes | No | 41 | H. sapiens M. musculus | [35] |
| RAM-ESVM | m6A | SVM | None | PseDNC Motif features | 1307 | Non-single-nucleotide resolution | Jackknife test | http://server.malab.cn/RAM-ESVM/ | Yes | No | 51 | S. cerevisiae | [46] |
| iRNA-PseColl | m6A | SVM | None | NCP ANF | 1130 | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/iRNA-PseColl/ | Yes | NA | 41 | H. sapiens | [47] |
| RAM-NPPS | m6A | SVM | RFE FSDI MRMD | NPPS | 8366 (H. sapiens) 1307 (S. cerevisiae) 394 (A. thaliana) | Mixed | Jackknife test | http://server.malab.cn/RAM-NPPS/ | Yes | No | 51 | H. sapiens S. cerevisiae A. thaliana | [26] |
| iMethyl-STTNC | m6A | SVM | None | STTNC | 1307 | Non-single-nucleotide resolution | Jackknife test | No | No | No | 51 | S. cerevisiae | [48] |
| iRNA(m6A)-PseDNC | m6A | SVM | None | PseDNC | 1307 | Non-single-nucleotide resolution | 10-fold cross-validation | http://lin-group.cn/server/iRNA(m6A)-PseDNC.php | Yes | No | 51 | S. cerevisiae | [49] |
| BERMP | m6A | BGRU | None | ENAC RNA word embedding | 53,000 (Mammalian full transcript mode) 44,853 (Mammalian Mature mRNA mode) 1100 (S. cerevisiae) 2100 (A. thaliana) | Mixed | 10-fold cross-validation | http://www.bioinfogo.org/bermp | Yes | Low Moderate High Very high | 251 (Mammalian) 51 (S. cerevisiae) 101 (Arabidopsis thaliana) | H. sapiens M. musculus S. cerevisiae A. thaliana | [38] |
| M6AMRFS | m6A | XGBoost | SFS | Dinucleotide binary Local position-specific dinucleotide frequency | 1307 (S. cerevisiae) 1130 (H. sapiens) 725 (M. musculus) 1000 (A. thaliana) | Non-single-nucleotide resolution | 10-fold cross-validation jackknife test | http://server.malab.cn/M6AMRFS/ | Yes | No | 51 (S. cerevisiae) 41 (H. sapiens) 41 (M. musculus) 25 (A. thaliana) | S. cerevisiae H. sapiens M. musculus A. thaliana | [50] |
| RFAthM6A | m6A | RF | None | PSNSP PSDSP KSNPF k-mer | 2518 | Non-single-nucleotide resolution | Fivefold cross-validation Independent test | Rscript | Yes | NA | 101 | A. thaliana | [27] |
| M6APred-EL | m6A | Ensemble of SVM | None | PS(k-mer)NP PCPs RFHC-GACs | 1307 | Non-single-nucleotide resolution | 10-fold cross-validation | http://server.malab.cn/M6APred-EL/ | Yes | No | 51 | S. cerevisiae | [51] |
| — | m6A | SVM | None | NCP ANF | 2055 | Non-single-nucleotide resolution | 10-fold cross-validation Independent test | No | No | No | 41 | E. coli | [52] |
| HMpre | m6A | XGBoost | None | Site Location Entropy Information SNP features Binary CPD Kmers | 26,512 | Single- nucleotide resolution | 10-fold cross-validation Independent test | No | No | No | 51 | H. sapiens | [53] |
| WHISTLE | m6A | SVM | Perturb method | NCP CNF Genome-derived features | 20,516 17,383 | Single- nucleotide resolution | Fivefold cross-validation Independent test | www.xjtlu.edu.cn/biologicalsciences/whistle http://whistle-epitranscriptome.com | No | No | NA | H. sapiens | [39] |
| DeepM6APred | m6A | SVM | None | Deep features NPPS | 1307 | Non-single-nucleotide resolution | 10-fold cross-validation | http://server.malab.cn/DeepM6APred/ | Yes | No | 51 | S. cerevisiae | [54] |
| Gene2Vec | m6A | CNN | None | One-hot Neighbouring methylation state RNA word embedding Gene2vec | 56,557 | Single- nucleotide resolution | Training and validation | http://server.malab.cn/Gene2vec/ | Yes | No | 1001 | H. sapiens M. musculus | [37] |
| Tool . | Modification . | Algorithm . | Feature selection . | Encoding scheme(s) . | Benchmark dataset size (modification sites) . | Dataset quality . | Evaluation strategy . | URL/stand-alone package . | Option of batch prediction . | Adjustment of predictor thresholds . | Window size . | Species . | Reference . |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RAMPred | m1A | SVM | None | NCP ANF | 6366 (H. sapiens) 1064 (M. musculus) 483 (S. cerevisiae) | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/RAMPred | Yes | No | 41 | H. sapiens M. musculus S. cerevisiae | [40] |
| iRNA-3typeA | m1A m6A | SVM | None | NCP ANF | 6366 (H. sapiens; m1A) 1064 (M. musculus; m1A) 1130 (H. sapiens; m6A) 725 (M. musculus; m6A) | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/iRNA-3typeA/ | Yes | No | 41 | H. sapiens M. musculus | [41] |
| iRNA-Methyl | m6A | SVM | None | PseDNC RNA property parameters | 1307 | Non-single-nucleotide resolution | 10-fold cross-validation Jackknife test | http://lin-group.cn/server/iRNA-Methyl | Yes | No | 51 | S. cerevisiae | [42] |
| m6Apred | m6A | SVM | None | NCP ANF | 1307 (832/475) | Non-single-nucleotide resolution | Jackknife test Independent test | http://lin-group.cn/server/m6Apred.php | Yes | All High Medium Low | 21 | S. cerevisiae | [43] |
| M6ATH | m6A | SVM | None | NCP ANF | 394 | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/M6ATH | Yes | No | 25 | A. thaliana | [29] |
| RNA-MethylPred | m6A | SVM | None | BPB DNC KNN score | 1307 | Non-single-nucleotide resolution | Jackknife test | MATLAB package | No | No | 51 | S. cerevisiae | [33] |
| TargetM6A | m6A | SVM | IFS | PSNP PSDP k-mer | 1307 (Met2614) 832 (Train1664) | Non-single-nucleotide resolution | Jackknife test | http://csbio.njust.edu.cn/bioinf/TargetM6A (Not available) | No | No | 51/21 | S. cerevisiae | [32] |
| pRNAm-PC | m6A | SVM | None | PCPM | 1307 | Non-single-nucleotide resolution | Jackknife test | http://www.jci-bioinfo.cn/pRNAm-PC | Yes | No | 51 | S. cerevisiae | [44] |
| RNAMethPre | m6A | SVM | None | binary k-mer Relative position value MFE | 29,457 (H. sapiens) 31,728 (Mouse) | Single- nucleotide resolution | Fivefold cross-validation Independent test | http://bioinfo.tsinghua.edu.cn/RNAMethPre/index.html (Not available) | NA | NA | 101 | H. sapiens M. musculus | [31] |
| AthMethPre | m6A | SVM | None | binary k-mer | 6581 | Non-single-nucleotide resolution | Fivefold cross-validation & Independent test | http://bioinfo.tsinghua.edu.cn/AthMethPre/index.html (Not available) | NA | NA | 101 | A. thaliana | [30] |
| M6A-HPCS | m6A | SVM | None | PCPM PseDNC AC CC | 1307 | Non-single-nucleotide resolution | Jackknife test 10-fold cross-validation | http://csbio.njust.edu.cn/bioinf/M6A-HPCS (Not available) | NA | NA | 51 | S. cerevisiae | [45] |
| SRAMP | m6A | RF | None | binary KNN score spectrum | 55,706 (Full transcript mode) 46,992 (Mature mRNA mode) | Single- nucleotide resolution | Fivefold cross-validation | http://www.cuilab.cn/sramp/ | No | No | 251 | H. sapiens M. musculus | [36] |
| MethyRNA | m6A | SVM | None | NCP ANF | 1130 (H. sapiens) 725 (M. musculus) | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/methyrna | Yes | No | 41 | H. sapiens M. musculus | [35] |
| RAM-ESVM | m6A | SVM | None | PseDNC Motif features | 1307 | Non-single-nucleotide resolution | Jackknife test | http://server.malab.cn/RAM-ESVM/ | Yes | No | 51 | S. cerevisiae | [46] |
| iRNA-PseColl | m6A | SVM | None | NCP ANF | 1130 | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/iRNA-PseColl/ | Yes | NA | 41 | H. sapiens | [47] |
| RAM-NPPS | m6A | SVM | RFE FSDI MRMD | NPPS | 8366 (H. sapiens) 1307 (S. cerevisiae) 394 (A. thaliana) | Mixed | Jackknife test | http://server.malab.cn/RAM-NPPS/ | Yes | No | 51 | H. sapiens S. cerevisiae A. thaliana | [26] |
| iMethyl-STTNC | m6A | SVM | None | STTNC | 1307 | Non-single-nucleotide resolution | Jackknife test | No | No | No | 51 | S. cerevisiae | [48] |
| iRNA(m6A)-PseDNC | m6A | SVM | None | PseDNC | 1307 | Non-single-nucleotide resolution | 10-fold cross-validation | http://lin-group.cn/server/iRNA(m6A)-PseDNC.php | Yes | No | 51 | S. cerevisiae | [49] |
| BERMP | m6A | BGRU | None | ENAC RNA word embedding | 53,000 (Mammalian full transcript mode) 44,853 (Mammalian Mature mRNA mode) 1100 (S. cerevisiae) 2100 (A. thaliana) | Mixed | 10-fold cross-validation | http://www.bioinfogo.org/bermp | Yes | Low Moderate High Very high | 251 (Mammalian) 51 (S. cerevisiae) 101 (Arabidopsis thaliana) | H. sapiens M. musculus S. cerevisiae A. thaliana | [38] |
| M6AMRFS | m6A | XGBoost | SFS | Dinucleotide binary Local position-specific dinucleotide frequency | 1307 (S. cerevisiae) 1130 (H. sapiens) 725 (M. musculus) 1000 (A. thaliana) | Non-single-nucleotide resolution | 10-fold cross-validation jackknife test | http://server.malab.cn/M6AMRFS/ | Yes | No | 51 (S. cerevisiae) 41 (H. sapiens) 41 (M. musculus) 25 (A. thaliana) | S. cerevisiae H. sapiens M. musculus A. thaliana | [50] |
| RFAthM6A | m6A | RF | None | PSNSP PSDSP KSNPF k-mer | 2518 | Non-single-nucleotide resolution | Fivefold cross-validation Independent test | Rscript | Yes | NA | 101 | A. thaliana | [27] |
| M6APred-EL | m6A | Ensemble of SVM | None | PS(k-mer)NP PCPs RFHC-GACs | 1307 | Non-single-nucleotide resolution | 10-fold cross-validation | http://server.malab.cn/M6APred-EL/ | Yes | No | 51 | S. cerevisiae | [51] |
| — | m6A | SVM | None | NCP ANF | 2055 | Non-single-nucleotide resolution | 10-fold cross-validation Independent test | No | No | No | 41 | E. coli | [52] |
| HMpre | m6A | XGBoost | None | Site Location Entropy Information SNP features Binary CPD Kmers | 26,512 | Single- nucleotide resolution | 10-fold cross-validation Independent test | No | No | No | 51 | H. sapiens | [53] |
| WHISTLE | m6A | SVM | Perturb method | NCP CNF Genome-derived features | 20,516 17,383 | Single- nucleotide resolution | Fivefold cross-validation Independent test | www.xjtlu.edu.cn/biologicalsciences/whistle http://whistle-epitranscriptome.com | No | No | NA | H. sapiens | [39] |
| DeepM6APred | m6A | SVM | None | Deep features NPPS | 1307 | Non-single-nucleotide resolution | 10-fold cross-validation | http://server.malab.cn/DeepM6APred/ | Yes | No | 51 | S. cerevisiae | [54] |
| Gene2Vec | m6A | CNN | None | One-hot Neighbouring methylation state RNA word embedding Gene2vec | 56,557 | Single- nucleotide resolution | Training and validation | http://server.malab.cn/Gene2vec/ | Yes | No | 1001 | H. sapiens M. musculus | [37] |
Abbreviations: PseDNC, pseudo dinucleotide composition; NCP, nucleotide chemical property; ANF, accumulated nucleotide frequency; BPB, bi-profile bayes; DNC, dinucleotide composition; KNN, k nearest neighbour; PSNP, position-specific nucleotide propensity; PSDP, position-specific dinucleotide propensity; NC, nucleotide composition; MFE, minimum free energy; PCPM, physical-chemical property matrix; AC, auto-covariance; CC, cross-covariance; NPPS, nucleotide pair position specificity; STTNC, split-tetra-nucleotide composition; ENAC, Enhanced nucleic acid composition; PSNSP, position-specific nucleotide sequence profile; PSDSP, position-specific dinucleotide sequence profile; KSNPF, K-spaced nucleotide pair frequencies; PS(k-mer) NP, position-specific k-mer nucleotide propensity; PCPs, physical-chemical properties; RFHC-GACs, ring-function-hydrogen-chemical properties without GAC; CPD, chemical property with density; IFS, incremental feature selection; RFE, recursive feature elimination; FSDI, feature selection based on discernibility and independence of a feature; MRMD, maximal relevance and maximal distance; SFS, sequence forward search.
| Tool . | Modification . | Algorithm . | Feature selection . | Encoding scheme(s) . | Benchmark dataset size (modification sites) . | Dataset quality . | Evaluation strategy . | URL/stand-alone package . | Option of batch prediction . | Adjustment of predictor thresholds . | Window size . | Species . | Reference . |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RAMPred | m1A | SVM | None | NCP ANF | 6366 (H. sapiens) 1064 (M. musculus) 483 (S. cerevisiae) | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/RAMPred | Yes | No | 41 | H. sapiens M. musculus S. cerevisiae | [40] |
| iRNA-3typeA | m1A m6A | SVM | None | NCP ANF | 6366 (H. sapiens; m1A) 1064 (M. musculus; m1A) 1130 (H. sapiens; m6A) 725 (M. musculus; m6A) | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/iRNA-3typeA/ | Yes | No | 41 | H. sapiens M. musculus | [41] |
| iRNA-Methyl | m6A | SVM | None | PseDNC RNA property parameters | 1307 | Non-single-nucleotide resolution | 10-fold cross-validation Jackknife test | http://lin-group.cn/server/iRNA-Methyl | Yes | No | 51 | S. cerevisiae | [42] |
| m6Apred | m6A | SVM | None | NCP ANF | 1307 (832/475) | Non-single-nucleotide resolution | Jackknife test Independent test | http://lin-group.cn/server/m6Apred.php | Yes | All High Medium Low | 21 | S. cerevisiae | [43] |
| M6ATH | m6A | SVM | None | NCP ANF | 394 | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/M6ATH | Yes | No | 25 | A. thaliana | [29] |
| RNA-MethylPred | m6A | SVM | None | BPB DNC KNN score | 1307 | Non-single-nucleotide resolution | Jackknife test | MATLAB package | No | No | 51 | S. cerevisiae | [33] |
| TargetM6A | m6A | SVM | IFS | PSNP PSDP k-mer | 1307 (Met2614) 832 (Train1664) | Non-single-nucleotide resolution | Jackknife test | http://csbio.njust.edu.cn/bioinf/TargetM6A (Not available) | No | No | 51/21 | S. cerevisiae | [32] |
| pRNAm-PC | m6A | SVM | None | PCPM | 1307 | Non-single-nucleotide resolution | Jackknife test | http://www.jci-bioinfo.cn/pRNAm-PC | Yes | No | 51 | S. cerevisiae | [44] |
| RNAMethPre | m6A | SVM | None | binary k-mer Relative position value MFE | 29,457 (H. sapiens) 31,728 (Mouse) | Single- nucleotide resolution | Fivefold cross-validation Independent test | http://bioinfo.tsinghua.edu.cn/RNAMethPre/index.html (Not available) | NA | NA | 101 | H. sapiens M. musculus | [31] |
| AthMethPre | m6A | SVM | None | binary k-mer | 6581 | Non-single-nucleotide resolution | Fivefold cross-validation & Independent test | http://bioinfo.tsinghua.edu.cn/AthMethPre/index.html (Not available) | NA | NA | 101 | A. thaliana | [30] |
| M6A-HPCS | m6A | SVM | None | PCPM PseDNC AC CC | 1307 | Non-single-nucleotide resolution | Jackknife test 10-fold cross-validation | http://csbio.njust.edu.cn/bioinf/M6A-HPCS (Not available) | NA | NA | 51 | S. cerevisiae | [45] |
| SRAMP | m6A | RF | None | binary KNN score spectrum | 55,706 (Full transcript mode) 46,992 (Mature mRNA mode) | Single- nucleotide resolution | Fivefold cross-validation | http://www.cuilab.cn/sramp/ | No | No | 251 | H. sapiens M. musculus | [36] |
| MethyRNA | m6A | SVM | None | NCP ANF | 1130 (H. sapiens) 725 (M. musculus) | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/methyrna | Yes | No | 41 | H. sapiens M. musculus | [35] |
| RAM-ESVM | m6A | SVM | None | PseDNC Motif features | 1307 | Non-single-nucleotide resolution | Jackknife test | http://server.malab.cn/RAM-ESVM/ | Yes | No | 51 | S. cerevisiae | [46] |
| iRNA-PseColl | m6A | SVM | None | NCP ANF | 1130 | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/iRNA-PseColl/ | Yes | NA | 41 | H. sapiens | [47] |
| RAM-NPPS | m6A | SVM | RFE FSDI MRMD | NPPS | 8366 (H. sapiens) 1307 (S. cerevisiae) 394 (A. thaliana) | Mixed | Jackknife test | http://server.malab.cn/RAM-NPPS/ | Yes | No | 51 | H. sapiens S. cerevisiae A. thaliana | [26] |
| iMethyl-STTNC | m6A | SVM | None | STTNC | 1307 | Non-single-nucleotide resolution | Jackknife test | No | No | No | 51 | S. cerevisiae | [48] |
| iRNA(m6A)-PseDNC | m6A | SVM | None | PseDNC | 1307 | Non-single-nucleotide resolution | 10-fold cross-validation | http://lin-group.cn/server/iRNA(m6A)-PseDNC.php | Yes | No | 51 | S. cerevisiae | [49] |
| BERMP | m6A | BGRU | None | ENAC RNA word embedding | 53,000 (Mammalian full transcript mode) 44,853 (Mammalian Mature mRNA mode) 1100 (S. cerevisiae) 2100 (A. thaliana) | Mixed | 10-fold cross-validation | http://www.bioinfogo.org/bermp | Yes | Low Moderate High Very high | 251 (Mammalian) 51 (S. cerevisiae) 101 (Arabidopsis thaliana) | H. sapiens M. musculus S. cerevisiae A. thaliana | [38] |
| M6AMRFS | m6A | XGBoost | SFS | Dinucleotide binary Local position-specific dinucleotide frequency | 1307 (S. cerevisiae) 1130 (H. sapiens) 725 (M. musculus) 1000 (A. thaliana) | Non-single-nucleotide resolution | 10-fold cross-validation jackknife test | http://server.malab.cn/M6AMRFS/ | Yes | No | 51 (S. cerevisiae) 41 (H. sapiens) 41 (M. musculus) 25 (A. thaliana) | S. cerevisiae H. sapiens M. musculus A. thaliana | [50] |
| RFAthM6A | m6A | RF | None | PSNSP PSDSP KSNPF k-mer | 2518 | Non-single-nucleotide resolution | Fivefold cross-validation Independent test | Rscript | Yes | NA | 101 | A. thaliana | [27] |
| M6APred-EL | m6A | Ensemble of SVM | None | PS(k-mer)NP PCPs RFHC-GACs | 1307 | Non-single-nucleotide resolution | 10-fold cross-validation | http://server.malab.cn/M6APred-EL/ | Yes | No | 51 | S. cerevisiae | [51] |
| — | m6A | SVM | None | NCP ANF | 2055 | Non-single-nucleotide resolution | 10-fold cross-validation Independent test | No | No | No | 41 | E. coli | [52] |
| HMpre | m6A | XGBoost | None | Site Location Entropy Information SNP features Binary CPD Kmers | 26,512 | Single- nucleotide resolution | 10-fold cross-validation Independent test | No | No | No | 51 | H. sapiens | [53] |
| WHISTLE | m6A | SVM | Perturb method | NCP CNF Genome-derived features | 20,516 17,383 | Single- nucleotide resolution | Fivefold cross-validation Independent test | www.xjtlu.edu.cn/biologicalsciences/whistle http://whistle-epitranscriptome.com | No | No | NA | H. sapiens | [39] |
| DeepM6APred | m6A | SVM | None | Deep features NPPS | 1307 | Non-single-nucleotide resolution | 10-fold cross-validation | http://server.malab.cn/DeepM6APred/ | Yes | No | 51 | S. cerevisiae | [54] |
| Gene2Vec | m6A | CNN | None | One-hot Neighbouring methylation state RNA word embedding Gene2vec | 56,557 | Single- nucleotide resolution | Training and validation | http://server.malab.cn/Gene2vec/ | Yes | No | 1001 | H. sapiens M. musculus | [37] |
| Tool . | Modification . | Algorithm . | Feature selection . | Encoding scheme(s) . | Benchmark dataset size (modification sites) . | Dataset quality . | Evaluation strategy . | URL/stand-alone package . | Option of batch prediction . | Adjustment of predictor thresholds . | Window size . | Species . | Reference . |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RAMPred | m1A | SVM | None | NCP ANF | 6366 (H. sapiens) 1064 (M. musculus) 483 (S. cerevisiae) | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/RAMPred | Yes | No | 41 | H. sapiens M. musculus S. cerevisiae | [40] |
| iRNA-3typeA | m1A m6A | SVM | None | NCP ANF | 6366 (H. sapiens; m1A) 1064 (M. musculus; m1A) 1130 (H. sapiens; m6A) 725 (M. musculus; m6A) | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/iRNA-3typeA/ | Yes | No | 41 | H. sapiens M. musculus | [41] |
| iRNA-Methyl | m6A | SVM | None | PseDNC RNA property parameters | 1307 | Non-single-nucleotide resolution | 10-fold cross-validation Jackknife test | http://lin-group.cn/server/iRNA-Methyl | Yes | No | 51 | S. cerevisiae | [42] |
| m6Apred | m6A | SVM | None | NCP ANF | 1307 (832/475) | Non-single-nucleotide resolution | Jackknife test Independent test | http://lin-group.cn/server/m6Apred.php | Yes | All High Medium Low | 21 | S. cerevisiae | [43] |
| M6ATH | m6A | SVM | None | NCP ANF | 394 | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/M6ATH | Yes | No | 25 | A. thaliana | [29] |
| RNA-MethylPred | m6A | SVM | None | BPB DNC KNN score | 1307 | Non-single-nucleotide resolution | Jackknife test | MATLAB package | No | No | 51 | S. cerevisiae | [33] |
| TargetM6A | m6A | SVM | IFS | PSNP PSDP k-mer | 1307 (Met2614) 832 (Train1664) | Non-single-nucleotide resolution | Jackknife test | http://csbio.njust.edu.cn/bioinf/TargetM6A (Not available) | No | No | 51/21 | S. cerevisiae | [32] |
| pRNAm-PC | m6A | SVM | None | PCPM | 1307 | Non-single-nucleotide resolution | Jackknife test | http://www.jci-bioinfo.cn/pRNAm-PC | Yes | No | 51 | S. cerevisiae | [44] |
| RNAMethPre | m6A | SVM | None | binary k-mer Relative position value MFE | 29,457 (H. sapiens) 31,728 (Mouse) | Single- nucleotide resolution | Fivefold cross-validation Independent test | http://bioinfo.tsinghua.edu.cn/RNAMethPre/index.html (Not available) | NA | NA | 101 | H. sapiens M. musculus | [31] |
| AthMethPre | m6A | SVM | None | binary k-mer | 6581 | Non-single-nucleotide resolution | Fivefold cross-validation & Independent test | http://bioinfo.tsinghua.edu.cn/AthMethPre/index.html (Not available) | NA | NA | 101 | A. thaliana | [30] |
| M6A-HPCS | m6A | SVM | None | PCPM PseDNC AC CC | 1307 | Non-single-nucleotide resolution | Jackknife test 10-fold cross-validation | http://csbio.njust.edu.cn/bioinf/M6A-HPCS (Not available) | NA | NA | 51 | S. cerevisiae | [45] |
| SRAMP | m6A | RF | None | binary KNN score spectrum | 55,706 (Full transcript mode) 46,992 (Mature mRNA mode) | Single- nucleotide resolution | Fivefold cross-validation | http://www.cuilab.cn/sramp/ | No | No | 251 | H. sapiens M. musculus | [36] |
| MethyRNA | m6A | SVM | None | NCP ANF | 1130 (H. sapiens) 725 (M. musculus) | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/methyrna | Yes | No | 41 | H. sapiens M. musculus | [35] |
| RAM-ESVM | m6A | SVM | None | PseDNC Motif features | 1307 | Non-single-nucleotide resolution | Jackknife test | http://server.malab.cn/RAM-ESVM/ | Yes | No | 51 | S. cerevisiae | [46] |
| iRNA-PseColl | m6A | SVM | None | NCP ANF | 1130 | Non-single-nucleotide resolution | Jackknife test | http://lin-group.cn/server/iRNA-PseColl/ | Yes | NA | 41 | H. sapiens | [47] |
| RAM-NPPS | m6A | SVM | RFE FSDI MRMD | NPPS | 8366 (H. sapiens) 1307 (S. cerevisiae) 394 (A. thaliana) | Mixed | Jackknife test | http://server.malab.cn/RAM-NPPS/ | Yes | No | 51 | H. sapiens S. cerevisiae A. thaliana | [26] |
| iMethyl-STTNC | m6A | SVM | None | STTNC | 1307 | Non-single-nucleotide resolution | Jackknife test | No | No | No | 51 | S. cerevisiae | [48] |
| iRNA(m6A)-PseDNC | m6A | SVM | None | PseDNC | 1307 | Non-single-nucleotide resolution | 10-fold cross-validation | http://lin-group.cn/server/iRNA(m6A)-PseDNC.php | Yes | No | 51 | S. cerevisiae | [49] |
| BERMP | m6A | BGRU | None | ENAC RNA word embedding | 53,000 (Mammalian full transcript mode) 44,853 (Mammalian Mature mRNA mode) 1100 (S. cerevisiae) 2100 (A. thaliana) | Mixed | 10-fold cross-validation | http://www.bioinfogo.org/bermp | Yes | Low Moderate High Very high | 251 (Mammalian) 51 (S. cerevisiae) 101 (Arabidopsis thaliana) | H. sapiens M. musculus S. cerevisiae A. thaliana | [38] |
| M6AMRFS | m6A | XGBoost | SFS | Dinucleotide binary Local position-specific dinucleotide frequency | 1307 (S. cerevisiae) 1130 (H. sapiens) 725 (M. musculus) 1000 (A. thaliana) | Non-single-nucleotide resolution | 10-fold cross-validation jackknife test | http://server.malab.cn/M6AMRFS/ | Yes | No | 51 (S. cerevisiae) 41 (H. sapiens) 41 (M. musculus) 25 (A. thaliana) | S. cerevisiae H. sapiens M. musculus A. thaliana | [50] |
| RFAthM6A | m6A | RF | None | PSNSP PSDSP KSNPF k-mer | 2518 | Non-single-nucleotide resolution | Fivefold cross-validation Independent test | Rscript | Yes | NA | 101 | A. thaliana | [27] |
| M6APred-EL | m6A | Ensemble of SVM | None | PS(k-mer)NP PCPs RFHC-GACs | 1307 | Non-single-nucleotide resolution | 10-fold cross-validation | http://server.malab.cn/M6APred-EL/ | Yes | No | 51 | S. cerevisiae | [51] |
| — | m6A | SVM | None | NCP ANF | 2055 | Non-single-nucleotide resolution | 10-fold cross-validation Independent test | No | No | No | 41 | E. coli | [52] |
| HMpre | m6A | XGBoost | None | Site Location Entropy Information SNP features Binary CPD Kmers | 26,512 | Single- nucleotide resolution | 10-fold cross-validation Independent test | No | No | No | 51 | H. sapiens | [53] |
| WHISTLE | m6A | SVM | Perturb method | NCP CNF Genome-derived features | 20,516 17,383 | Single- nucleotide resolution | Fivefold cross-validation Independent test | www.xjtlu.edu.cn/biologicalsciences/whistle http://whistle-epitranscriptome.com | No | No | NA | H. sapiens | [39] |
| DeepM6APred | m6A | SVM | None | Deep features NPPS | 1307 | Non-single-nucleotide resolution | 10-fold cross-validation | http://server.malab.cn/DeepM6APred/ | Yes | No | 51 | S. cerevisiae | [54] |
| Gene2Vec | m6A | CNN | None | One-hot Neighbouring methylation state RNA word embedding Gene2vec | 56,557 | Single- nucleotide resolution | Training and validation | http://server.malab.cn/Gene2vec/ | Yes | No | 1001 | H. sapiens M. musculus | [37] |
Abbreviations: PseDNC, pseudo dinucleotide composition; NCP, nucleotide chemical property; ANF, accumulated nucleotide frequency; BPB, bi-profile bayes; DNC, dinucleotide composition; KNN, k nearest neighbour; PSNP, position-specific nucleotide propensity; PSDP, position-specific dinucleotide propensity; NC, nucleotide composition; MFE, minimum free energy; PCPM, physical-chemical property matrix; AC, auto-covariance; CC, cross-covariance; NPPS, nucleotide pair position specificity; STTNC, split-tetra-nucleotide composition; ENAC, Enhanced nucleic acid composition; PSNSP, position-specific nucleotide sequence profile; PSDSP, position-specific dinucleotide sequence profile; KSNPF, K-spaced nucleotide pair frequencies; PS(k-mer) NP, position-specific k-mer nucleotide propensity; PCPs, physical-chemical properties; RFHC-GACs, ring-function-hydrogen-chemical properties without GAC; CPD, chemical property with density; IFS, incremental feature selection; RFE, recursive feature elimination; FSDI, feature selection based on discernibility and independence of a feature; MRMD, maximal relevance and maximal distance; SFS, sequence forward search.
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