BMC Bioinformatics

Table 1 SVM performance on the complete tRNA-136 and randomly selected tRNA-136 dataset using the same parameter (-z c -t 2 -g 0.05 -c 2 -j 2)

From: Prediction of uridine modifications in tRNA sequences

Threshold	Complete tRNA-136 dataset				Randomized tRNA-136 dataset
Threshold	SN	SP	ACC	MCC	SN	SP	ACC	MCC
−1.00	96.37	60.89	70.42	0.51	97.24	78.59	80.30	0.49
−0.90	95.31	70.16	76.91	0.58	96.68	85.80	86.80	0.58
−0.80	94.25	76.37	81.17	0.63	96.13	90.13	90.68	0.65
−0.70	93.64	80.42	83.97	0.67	*93.36*	*92.96*	*93.00*	*0.70*
−0.60	92.13	83.30	85.67	0.69	91.71	94.56	94.31	0.73
−0.50	91.37	85.14	86.81	0.71	89.52	95.73	95.16	0.76
−0.40	90.31	86.63	87.62	0.72	88.44	96.51	95.77	0.78
−0.30	89.40	87.80	88.23	0.73	87.34	96.89	96.02	0.78
−0.20	*88.64*	*89.35*	*89.17*	*0.75*	85.72	97.34	96.27	0.79
−0.10	87.43	90.57	89.73	0.75	84.07	97.67	96.42	0.79
0.00	85.92	91.68	90.14	0.76	80.80	98.17	96.58	0.79
0.10	83.80	92.57	90.22	0.75	75.82	98.56	96.47	0.78
0.20	81.08	93.01	89.81	0.74	74.71	98.78	96.58	0.78
0.30	79.72	93.62	89.90	0.74	71.44	98.89	96.37	0.77
0.40	76.70	94.34	89.61	0.73	68.69	99.00	96.22	0.76
0.50	73.67	95.28	89.49	0.72	62.69	99.11	95.77	0.72
0.60	69.43	95.89	88.80	0.70	58.27	99.33	95.57	0.70
0.70	65.20	96.67	88.23	0.69	53.87	99.33	95.16	0.67
0.80	59.00	97.28	87.01	0.65	45.11	99.39	94.41	0.61
0.90	51.59	97.78	85.39	0.60	32.40	99.45	93.30	0.50
1.00	40.84	98.39	82.95	0.53	26.37	99.72	93.00	0.46

Bold are performances with maximum MCC (Threshold 0.0 or close to 0.0 preferred).
Bold and italic are performances where gap between sensitivity and specificity are minimum.

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