CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PknotsRG		IPknot
MCC	0.623	>	0.612
Average MCC ± 95% Confidence Intervals	0.636 ± 0.237	>	0.588 ± 0.219
Sensitivity	0.645	>	0.579
Positive Predictive Value	0.615	<	0.658
Total TP	118	>	106
Total TN	11343	<	11374
Total FP	88	>	66
Total FP CONTRA	28	>	17
Total FP INCONS	46	>	38
Total FP COMP	14	>	11
Total FN	65	<	77
P-value	0.0

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

Total Scores
MCC	0.623
Average MCC ± 95% Confidence Intervals	0.636 ± 0.237
Sensitivity	0.645
Positive Predictive Value	0.615
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...	0.66	0.61	0.73	11	513	4	2	2	0	7
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	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...	0.73	0.72	0.75	21	1505	7	4	3	0	8
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	43	11	20	12	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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

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