CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAalifold(seed)		PPfold(20)
MCC	0.581	>	0.576
Average MCC ± 95% Confidence Intervals	0.575 ± 0.089	<	0.576 ± 0.144
Sensitivity	0.362	<	0.423
Positive Predictive Value	0.938	>	0.790
Total TP	106	<	124
Total TN	43439	>	43395
Total FP	10	<	40
Total FP CONTRA	2	>	0
Total FP INCONS	5	<	33
Total FP COMP	3	<	7
Total FN	187	>	169
P-value	0.0

Comparison of performance of RNAalifold(seed) and PPfold(20). 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 RNAalifold(seed) and PPfold(20)).
Comparison of performance of RNAalifold(seed) and PPfold(20). 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 RNAalifold(seed) and PPfold(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(seed) and PPfold(20). 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 RNAalifold(seed) and PPfold(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(seed) and PPfold(20). 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 RNAalifold(seed) and PPfold(20)).

Total Scores
MCC	0.581
Average MCC ± 95% Confidence Intervals	0.575 ± 0.089
Sensitivity	0.362
Positive Predictive Value	0.938
Nr of predictions	9

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.59	0.40	0.89	8	981	1	0	1	0	12
3RKF_A	Purine links to Rfam database...	0.63	0.47	0.84	16	2192	3	1	2	0	18
3SD1_A	THF links to Rfam database...	0.58	0.40	0.85	17	3896	3	1	2	0	25
3ZEX_C	5_8S_rRNA links to Rfam database...	0.42	0.17	1.00	9	14187	0	0	0	0	43
4A1C_2	5_8S_rRNA links to Rfam database...	0.39	0.15	1.00	5	11776	2	0	0	2	28
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13
4FRG_B	AdoCbl-variant links to Rfam database...	0.73	0.53	1.00	17	3469	0	0	0	0	15

Total Scores
MCC	0.576
Average MCC ± 95% Confidence Intervals	0.576 ± 0.144
Sensitivity	0.423
Positive Predictive Value	0.790
Nr of predictions	9

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.63	0.45	0.90	9	980	1	0	1	0	11
3RKF_A	Purine links to Rfam database...	0.73	0.56	0.95	19	2191	1	0	1	0	15
3SD1_A	THF links to Rfam database...	0.68	0.52	0.88	22	3891	3	0	3	0	20
3ZEX_C	5_8S_rRNA links to Rfam database...	0.33	0.21	0.52	11	14175	12	0	10	2	41
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.15	0.29	5	11764	16	0	12	4	28
4AOB_A	SAM links to Rfam database...	0.74	0.60	0.93	25	4344	3	0	2	1	17
4ENB_A	crcB links to Rfam database...	0.56	0.37	0.88	7	1267	1	0	1	0	12
4ENC_A	crcB links to Rfam database...	0.58	0.42	0.80	8	1316	2	0	2	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.73	0.56	0.95	18	3467	1	0	1	0	14

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