CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		Pknots
MCC	0.612	>	0.605
Average MCC ± 95% Confidence Intervals	0.588 ± 0.219	<	0.633 ± 0.249
Sensitivity	0.579	<	0.623
Positive Predictive Value	0.658	>	0.600
Total TP	106	<	114
Total TN	11374	>	11345
Total FP	66	<	96
Total FP CONTRA	17	<	23
Total FP INCONS	38	<	53
Total FP COMP	11	<	20
Total FN	77	>	69
P-value	0.0

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

Total Scores
MCC	0.612
Average MCC ± 95% Confidence Intervals	0.588 ± 0.219
Sensitivity	0.579
Positive Predictive Value	0.658
Nr of predictions	9

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	0.33	0.55	6	517	5	1	4	0	12
3J0L_a	-	0.16	0.18	0.18	2	400	10	3	6	1	9
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.74	0.69	0.80	20	1508	5	0	5	0	9
3U4M_B	-	0.91	0.91	0.91	20	1254	3	2	0	1	2
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.25	0.22	5	4493	26	8	10	8	15
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.59	0.53	0.67	8	484	4	0	4	0	7

Total Scores
MCC	0.605
Average MCC ± 95% Confidence Intervals	0.633 ± 0.249
Sensitivity	0.623
Positive Predictive Value	0.600
Nr of predictions	9

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...	0.83	0.83	0.83	15	510	3	2	1	0	3
3J0L_a	-	0.35	0.36	0.36	4	400	8	3	4	1	7
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.78	0.76	0.81	22	1506	5	1	4	0	7
3U4M_B	-	0.33	0.36	0.32	8	1251	17	4	13	0	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.29	8	4488	36	9	11	16	12
4AOB_A	SAM links to Rfam database...	0.19	0.21	0.21	6	1409	23	3	19	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	2	0	0	2	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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