CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Pknots		RNASLOpt
MCC	0.517	>	0.449
Average MCC ± 95% Confidence Intervals	0.571 ± 0.319	>	0.484 ± 0.218
Sensitivity	0.546	>	0.438
Positive Predictive Value	0.504	>	0.475
Total TP	71	>	57
Total TN	8995	<	9016
Total FP	90	>	73
Total FP CONTRA	22	<	23
Total FP INCONS	48	>	40
Total FP COMP	20	>	10
Total FN	59	<	73
P-value	0.0

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

Total Scores
MCC	0.517
Average MCC ± 95% Confidence Intervals	0.571 ± 0.319
Sensitivity	0.546
Positive Predictive Value	0.504
Nr of predictions	7

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
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

Total Scores
MCC	0.449
Average MCC ± 95% Confidence Intervals	0.484 ± 0.218
Sensitivity	0.438
Positive Predictive Value	0.475
Nr of predictions	7

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...	0.48	0.39	0.64	7	517	4	0	4	0	11
3J0L_a	-	0.21	0.18	0.29	2	404	6	3	2	1	9
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.30	0.40	0.24	8	4482	35	13	13	9	12
4AOB_A	SAM links to Rfam database...	0.31	0.28	0.38	8	1416	13	3	10	0	21
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...	0.73	0.60	0.90	9	486	1	1	0	0	6

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