CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MXScarna(seed)		PPfold(seed)
MCC	0.612	>	0.207
Average MCC ± 95% Confidence Intervals	0.563 ± 0.136	>	0.105 ± 0.116
Sensitivity	0.553	>	0.070
Positive Predictive Value	0.685	>	0.634
Total TP	207	>	26
Total TN	31441	<	31702
Total FP	147	>	80
Total FP CONTRA	30	>	1
Total FP INCONS	65	>	14
Total FP COMP	52	<	65
Total FN	167	<	348
P-value	2.34821445183e-08

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

Total Scores
MCC	0.612
Average MCC ± 95% Confidence Intervals	0.563 ± 0.136
Sensitivity	0.553
Positive Predictive Value	0.685
Nr of predictions	16

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...	-0.03	0.00	0.00	0	518	12	0	10	2	18
3J20_0	tRNA links to Rfam database...	0.90	0.86	0.95	18	1200	1	1	0	0	3
3J3E_8	5_8S_rRNA links to Rfam database...	0.23	0.20	0.27	3	2731	14	3	5	6	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.48	0.47	0.50	9	4743	21	5	4	12	10
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.74	0.76	0.73	22	1503	9	4	4	1	7
3W1K_J	tRNA-Sec links to Rfam database...	0.92	0.90	0.93	28	1648	3	1	1	1	3
3W3S_B	tRNA-Sec links to Rfam database...	0.74	0.70	0.79	23	1960	7	0	6	1	10
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.31	0.50	9	5356	21	3	6	12	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.45	0.40	0.50	8	4500	20	4	4	12	12
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	10	2	5	3	9
4ENB_A	crcB links to Rfam database...	0.54	0.40	0.75	6	464	2	0	2	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	1	3	0	9
4FRG_B	AdoCbl-variant links to Rfam database...	0.49	0.42	0.59	10	1185	8	2	5	1	14
4FRN_A	AdoCbl-variant links to Rfam database...	0.70	0.68	0.73	19	1822	7	3	4	0	9
4JF2_A	preQ1-II links to Rfam database...	0.41	0.33	0.53	8	1067	8	1	6	1	16

Total Scores
MCC	0.207
Average MCC ± 95% Confidence Intervals	0.105 ± 0.116
Sensitivity	0.070
Positive Predictive Value	0.634
Nr of predictions	16

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...	0.49	0.33	0.75	6	520	2	0	2	0	12
3J20_0	tRNA links to Rfam database...	0.00	0.00	0.00	0	1219	0	0	0	0	21
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2742	6	0	0	6	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.19	0.11	0.33	2	4755	24	0	4	20	17
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
3W1K_J	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	1678	0	0	0	0	31
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	1989	0	0	0	0	33
3ZEX_C	5_8S_rRNA links to Rfam database...	0.15	0.07	0.33	2	5368	24	0	4	20	27
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
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	1848	0	0	0	0	28
4JF2_A	preQ1-II links to Rfam database...	0.76	0.63	0.94	15	1066	1	1	0	0	9

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