CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		MCFold
MCC	0.570	>	0.449
Average MCC ± 95% Confidence Intervals	0.498 ± 0.160	>	0.403 ± 0.146
Sensitivity	0.469	<	0.474
Positive Predictive Value	0.698	>	0.434
Total TP	199	<	201
Total TN	52981	>	52803
Total FP	96	<	298
Total FP CONTRA	11	<	39
Total FP INCONS	75	<	223
Total FP COMP	10	<	36
Total FN	225	>	223
P-value	1.02533530638e-08

Comparison of performance of IPknot and MCFold. 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 IPknot and MCFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and MCFold. 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 IPknot and MCFold).

Total Scores
MCC	0.570
Average MCC ± 95% Confidence Intervals	0.498 ± 0.160
Sensitivity	0.469
Positive Predictive Value	0.698
Nr of predictions	15

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...	0.40	0.30	0.55	6	1529	5	1	4	0	14
2LKR_A	-	0.84	0.77	0.91	30	6072	4	0	3	1	9
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_2	-	0.39	0.36	0.43	12	6188	18	2	14	2	21
3J0L_a	-	0.21	0.19	0.25	3	1116	9	1	8	0	13
3J0L_7	-	-0.01	0.00	0.00	0	1218	7	0	7	0	17
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.61	0.48	0.80	20	3891	5	0	5	0	22
3U4M_B	-	0.68	0.54	0.87	20	3137	3	1	2	0	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	26	4	17	5	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
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...	0.52	0.42	0.67	8	1314	4	0	4	0	11

Total Scores
MCC	0.449
Average MCC ± 95% Confidence Intervals	0.403 ± 0.146
Sensitivity	0.474
Positive Predictive Value	0.434
Nr of predictions	15

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...	0.41	0.45	0.39	9	1517	16	0	14	2	11
2LKR_A	-	0.93	0.92	0.95	36	6067	14	0	2	12	3
3AMU_B	tRNA links to Rfam database...	0.44	0.48	0.42	13	2972	18	2	16	0	14
3J0L_g	-	0.13	0.25	0.08	1	452	12	8	4	0	3
3J0L_2	-	0.21	0.24	0.18	8	6172	39	7	29	3	25
3J0L_a	-	0.16	0.19	0.17	3	1110	15	1	14	0	13
3J0L_7	-	-0.01	0.00	0.00	0	1206	19	4	15	0	17
3J16_L	tRNA links to Rfam database...	0.45	0.47	0.44	14	2743	19	1	17	1	16
3RKF_A	Purine links to Rfam database...	0.70	0.65	0.76	22	2182	7	1	6	0	12
3SD1_A	THF links to Rfam database...	0.33	0.33	0.35	14	3876	26	0	26	0	28
3U4M_B	-	0.59	0.59	0.59	22	3123	15	0	15	0	15
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.11	5	11735	56	10	31	15	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.67	0.71	36	7089	17	1	14	2	18
4ENB_A	crcB links to Rfam database...	0.61	0.63	0.60	12	1255	8	2	6	0	7
4ENC_A	crcB links to Rfam database...	0.28	0.32	0.27	6	1304	17	2	14	1	13

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