CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASLOpt		Vsfold4
MCC	0.443	>	0.408
Average MCC ± 95% Confidence Intervals	0.409 ± 0.141	>	0.408 ± 0.142
Sensitivity	0.365	>	0.340
Positive Predictive Value	0.547	>	0.498
Total TP	146	>	136
Total TN	51810	>	51804
Total FP	130	<	151
Total FP CONTRA	15	>	13
Total FP INCONS	106	<	124
Total FP COMP	9	<	14
Total FN	254	<	264
P-value	4.7488605325e-07

Comparison of performance of RNASLOpt and Vsfold4. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for RNASLOpt and Vsfold4).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASLOpt and Vsfold4. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for RNASLOpt and Vsfold4).

Total Scores
MCC	0.443
Average MCC ± 95% Confidence Intervals	0.409 ± 0.141
Sensitivity	0.365
Positive Predictive Value	0.547
Nr of predictions	14

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.47	0.35	0.64	7	1529	4	0	4	0	13
2LKR_A	-	0.68	0.62	0.75	24	6073	9	0	8	1	15
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_2	-	0.39	0.36	0.43	12	6188	18	2	14	2	21
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_a	-	0.26	0.19	0.38	3	1120	5	1	4	0	13
3J16_L	tRNA links to Rfam database...	0.53	0.40	0.71	12	2758	5	0	5	0	18
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.48	0.32	0.71	12	3553	5	0	5	0	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Total Scores
MCC	0.408
Average MCC ± 95% Confidence Intervals	0.408 ± 0.142
Sensitivity	0.340
Positive Predictive Value	0.498
Nr of predictions	14

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1527	13	0	13	0	20
2LKR_A	-	0.31	0.28	0.34	11	6073	21	3	18	0	28
3J0L_7	-	0.51	0.41	0.64	7	1214	4	0	4	0	10
3J0L_2	-	0.38	0.36	0.41	12	6187	18	3	14	1	21
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_a	-	0.39	0.31	0.50	5	1118	5	2	3	0	11
3J16_L	tRNA links to Rfam database...	0.82	0.67	1.00	20	2755	0	0	0	0	10
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.53	0.41	0.71	15	3549	6	1	5	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.28	0.24	0.33	8	11757	28	0	16	12	25
4A1C_3	5S_rRNA links to Rfam database...	0.26	0.22	0.32	12	7103	25	2	23	0	42
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1317	0	0	0	0	10

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.