CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(seed)		ProbKnot
MCC	0.586	>	0.553
Average MCC ± 95% Confidence Intervals	0.529 ± 0.095	<	0.579 ± 0.113
Sensitivity	0.374	<	0.511
Positive Predictive Value	0.921	>	0.603
Total TP	337	<	460
Total TN	227023	>	226626
Total FP	41	<	346
Total FP CONTRA	13	<	59
Total FP INCONS	16	<	244
Total FP COMP	12	<	43
Total FN	564	>	441
P-value	8.55066880689e-08

Comparison of performance of CentroidAlifold(seed) and ProbKnot. 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 CentroidAlifold(seed) and ProbKnot).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for CentroidAlifold(seed) and ProbKnot).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(seed) and ProbKnot. 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 CentroidAlifold(seed) and ProbKnot).

Total Scores
MCC	0.586
Average MCC ± 95% Confidence Intervals	0.529 ± 0.095
Sensitivity	0.374
Positive Predictive Value	0.921
Nr of predictions	21

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	861	0	0	0	0	18
2LC8_A	GP_knot1 links to Rfam database...	0.00	0.00	0.00	0	1540	0	0	0	0	20
2XQD_Y	tRNA links to Rfam database...	0.47	0.22	1.00	6	2844	0	0	0	0	21
3AKZ_H	tRNA links to Rfam database...	0.46	0.21	1.00	6	2695	0	0	0	0	22
3AMU_B	tRNA links to Rfam database...	0.47	0.22	1.00	6	2997	0	0	0	0	21
3IYQ_A	tmRNA links to Rfam database...	0.52	0.39	0.70	37	60673	21	10	6	5	57
3IZ4_A	tmRNA links to Rfam database...	0.58	0.39	0.88	51	70818	7	2	5	0	81
3IZF_C	5S_rRNA links to Rfam database...	0.54	0.30	1.00	16	6887	0	0	0	0	38
3J16_L	tRNA links to Rfam database...	0.45	0.20	1.00	6	2769	0	0	0	0	24
3NPB_A	SAM links to Rfam database...	0.71	0.54	0.93	25	6994	4	1	1	2	21
3O58_3	5_8S_rRNA links to Rfam database...	0.56	0.34	0.92	12	12390	1	0	1	0	23
3O58_2	5S_rRNA links to Rfam database...	0.65	0.42	1.00	16	7244	0	0	0	0	22
3PDR_A	ykoK links to Rfam database...	0.77	0.61	0.98	44	12835	3	0	1	2	28
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...	0.71	0.52	0.96	22	3893	1	0	1	0	20
3UZL_B	tRNA links to Rfam database...	0.40	0.16	1.00	6	3564	0	0	0	0	31
4A1C_3	5S_rRNA links to Rfam database...	0.54	0.30	1.00	16	7124	0	0	0	0	38
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.24	0.89	8	11772	3	0	1	2	25
4AOB_A	SAM links to Rfam database...	0.75	0.57	1.00	24	4347	1	0	0	1	18
4ENB_A	crcB links to Rfam database...	0.65	0.42	1.00	8	1267	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.65	0.42	1.00	8	1318	0	0	0	0	11

Total Scores
MCC	0.553
Average MCC ± 95% Confidence Intervals	0.579 ± 0.113
Sensitivity	0.511
Positive Predictive Value	0.603
Nr of predictions	21

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2XQD_Y	tRNA links to Rfam database...	0.90	0.81	1.00	22	2828	1	0	0	1	5
3AKZ_H	tRNA links to Rfam database...	0.73	0.75	0.72	21	2672	8	4	4	0	7
3AMU_B	tRNA links to Rfam database...	0.65	0.59	0.73	16	2981	8	0	6	2	11
3IYQ_A	tmRNA links to Rfam database...	0.28	0.31	0.26	29	60616	85	22	59	4	65
3IZ4_A	tmRNA links to Rfam database...	0.52	0.46	0.60	61	70774	46	6	35	5	71
3IZF_C	5S_rRNA links to Rfam database...	0.72	0.61	0.85	33	6864	6	0	6	0	21
3J16_L	tRNA links to Rfam database...	0.35	0.33	0.38	10	2749	16	1	15	0	20
3NPB_A	SAM links to Rfam database...	0.72	0.61	0.85	28	6988	8	1	4	3	18
3O58_3	5_8S_rRNA links to Rfam database...	0.31	0.34	0.29	12	12362	41	4	25	12	23
3O58_2	5S_rRNA links to Rfam database...	0.76	0.76	0.76	29	7222	10	3	6	1	9
3PDR_A	ykoK links to Rfam database...	0.74	0.64	0.85	46	12826	10	1	7	2	26
3RKF_A	Purine links to Rfam database...	0.73	0.59	0.91	20	2189	2	1	1	0	14
3SD1_A	THF links to Rfam database...	0.55	0.48	0.65	20	3885	11	2	9	0	22
3UZL_B	tRNA links to Rfam database...	0.73	0.62	0.85	23	3543	4	0	4	0	14
4A1C_3	5S_rRNA links to Rfam database...	0.73	0.61	0.87	33	7102	6	1	4	1	21
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.12	5	11738	49	7	31	11	28
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1263	1	1	0	0	8
4ENC_A	crcB links to Rfam database...	0.45	0.42	0.50	8	1310	8	1	7	0	11

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