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

BMC Bioinformatics

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

Methods	Datasets^a	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

^aThe numbers in the parentheses are the ratios between m5C and non-m5C sites of that dataset
^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

ISSN: 1471-2105