CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Contrafold		PPfold(seed)
MCC	0.666	>	0.122
Average MCC ± 95% Confidence Intervals	0.678 ± 0.146	>	0.053 ± 0.099
Sensitivity	0.658	>	0.029
Positive Predictive Value	0.684	>	0.538
Total TP	160	>	7
Total TN	15986	<	16207
Total FP	101	>	25
Total FP CONTRA	25	>	0
Total FP INCONS	49	>	6
Total FP COMP	27	>	19
Total FN	83	<	236
P-value	1.75835195567e-08

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

Total Scores
MCC	0.666
Average MCC ± 95% Confidence Intervals	0.678 ± 0.146
Sensitivity	0.658
Positive Predictive Value	0.684
Nr of predictions	11

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...	0.46	0.39	0.58	7	516	5	3	2	0	11
3AMU_B	tRNA links to Rfam database...	0.75	0.79	0.71	15	1136	9	0	6	3	4
3J16_L	tRNA links to Rfam database...	0.55	0.57	0.55	12	1137	10	3	7	0	9
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	5	4	0	9
3UZL_B	tRNA links to Rfam database...	0.90	0.88	0.93	14	1278	8	0	1	7	2
4A1C_3	5S_rRNA links to Rfam database...	0.81	0.81	0.81	30	2726	10	0	7	3	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	33	9	13	11	15
4AOB_A	SAM links to Rfam database...	0.53	0.52	0.56	15	1410	13	3	9	1	14
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	1	0	0	1	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	1	0	0	1	4

Total Scores
MCC	0.122
Average MCC ± 95% Confidence Intervals	0.053 ± 0.099
Sensitivity	0.029
Positive Predictive Value	0.538
Nr of predictions	11

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
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	1157	0	0	0	0	19
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	1159	0	0	0	0	21
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
3UZL_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	1293	0	0	0	0	16
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

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