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Table 1 Summarization of the existing methods for predicting m5C sites of RNA

From: m5CPred-SVM: a novel method for predicting m5C sites of RNA

Methods Datasetsa Algorithms Webserver availability Evaluation strategy Features Species
iRNA-m5C [26] 120 m5C + 120 non-m5C
97 m5C + 97 non-m5C
6289 m5C + 6289 non-m5C
211 m5C + 211 non-m5C
RF Yes (1) Jackknife test
(2) independent test
PseKNC
MNBE
KNFC
NV
H. sapiens
M.musculus
A. thaliana
S.cerevisiae
RNAm5Cfinder [25] All m5C sites recorded in GSE90963
GSE93749
GSE83432
RF Yes (1) Fivefold cross validation
(2) Independent test
MNBE H. sapiens
M. musculus
PEA-m5C [24] DatasetCV (1196:11960)
DatasetHT (100:100)
DatasetT1 (79:79)
DatasetT2 (73:73)
RF Yes (1) Tenfold cross validation
(2) Independent test
PseDNC
KNFC
MNBE
A. thaliana
RNAm5CPred [23] Met935 (127:808)
Met240 (120:120)
Met1900 (475:1425)
Test1157 (157:1000)
SVM Yes (1) Jackknife test
(2) Tenfold cross validation
(3) Independent test
KNF
KSNPF
PseDNC
H. sapiens
pM5CS-Comp-mRMR [22] 120 m5C and 120 non-m5C SVM No Jackknife test DNC,
TNC, Tetra-NC
H. sapiens
M5C-HPCR [21] Met1320(120:1200)b
Met1900 (475:1425)
Ensemble of SVM No Jackknife test PseDNC H. sapiens
iRNAm5C-PseDNC [20] Met1900 (475:1425) RF Yes Jackknife test PseDNC H. sapiens
m5C-PseDNC [19] Met1320(120:1200)b SVM No Jackknife test PseDNC H. sapiens
  1. aThe numbers in the parentheses are the ratios between m5C and non-m5C sites of that dataset
  2. bAlthough the ratio between m5C and non-m5C sites is 120:1320, but the final model is based on a balanced dataset with 120 m5C and 120 non-m5C sites