CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(20)		PPfold(seed)
MCC	0.681	>	0.023
Average MCC ± 95% Confidence Intervals	0.660 ± 0.163	>	0.008 ± 0.016
Sensitivity	0.671	>	0.003
Positive Predictive Value	0.701	>	0.200
Total TP	216	>	1
Total TN	22281	<	22584
Total FP	118	>	23
Total FP CONTRA	21	>	0
Total FP INCONS	71	>	4
Total FP COMP	26	>	19
Total FN	106	<	321
P-value	9.64686604905e-09

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

Total Scores
MCC	0.681
Average MCC ± 95% Confidence Intervals	0.660 ± 0.163
Sensitivity	0.671
Positive Predictive Value	0.701
Nr of predictions	13

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.71	0.74	0.70	14	1137	9	0	6	3	5
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_0	tRNA links to Rfam database...	0.68	0.71	0.65	15	1196	9	2	6	1	6
3J2L_3	5S_rRNA links to Rfam database...	0.80	0.79	0.82	27	2987	10	0	6	4	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...	0.68	0.69	0.69	20	1504	9	4	5	0	9
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2765	8	0	2	6	6
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	6	0	4	2	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.25	0.16	5	4485	33	9	17	7	15
4AOB_A	SAM links to Rfam database...	0.59	0.55	0.64	16	1412	10	3	6	1	13
4ENB_A	crcB links to Rfam database...	0.39	0.33	0.50	5	462	6	0	5	1	10
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.13	0.13	0.17	3	1184	15	2	13	0	21

Total Scores
MCC	0.023
Average MCC ± 95% Confidence Intervals	0.008 ± 0.016
Sensitivity	0.003
Positive Predictive Value	0.200
Nr of predictions	13

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	1157	0	0	0	0	19
3J20_1	tRNA links to Rfam database...	0.00	0.00	0.00	0	1112	0	0	0	0	20
3J20_0	tRNA links to Rfam database...	0.00	0.00	0.00	0	1219	0	0	0	0	21
3J2L_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	3020	0	0	0	0	34
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	866	0	0	0	0	24
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
3ZEX_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2796	0	0	0	0	35
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2763	0	0	0	0	37
4A1C_2	5_8S_rRNA links to Rfam database...	0.10	0.05	0.20	1	4511	23	0	4	19	19
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	1437	0	0	0	0	29
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	472	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	496	0	0	0	0	15
4FRG_B	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	1202	0	0	0	0	24

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