CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Murlet(20)		PPfold(seed)
MCC	0.671	>	0.046
Average MCC ± 95% Confidence Intervals	0.650 ± 0.138	>	0.018 ± 0.027
Sensitivity	0.598	>	0.009
Positive Predictive Value	0.761	>	0.273
Total TP	210	>	3
Total TN	27687	<	27952
Total FP	87	>	47
Total FP CONTRA	13	>	0
Total FP INCONS	53	>	8
Total FP COMP	21	<	39
Total FN	141	<	348
P-value	1.93248927742e-08

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

Total Scores
MCC	0.671
Average MCC ± 95% Confidence Intervals	0.650 ± 0.138
Sensitivity	0.598
Positive Predictive Value	0.761
Nr of predictions	14

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.89	0.89	0.89	17	1138	4	0	2	2	2
3J20_1	tRNA links to Rfam database...	0.69	0.60	0.80	12	1097	4	0	3	1	8
3J20_0	tRNA links to Rfam database...	0.65	0.62	0.68	13	1200	6	1	5	0	8
3J2L_3	5S_rRNA links to Rfam database...	0.84	0.74	0.96	25	2994	4	0	1	3	9
3RKF_A	Purine links to Rfam database...	0.81	0.67	1.00	16	850	0	0	0	0	8
3SD1_A	THF links to Rfam database...	0.82	0.83	0.83	24	1504	5	4	1	0	5
3ZEX_C	5_8S_rRNA links to Rfam database...	0.42	0.38	0.48	11	5351	16	2	10	4	18
3ZEX_D	5S_rRNA links to Rfam database...	0.90	0.86	0.94	30	2764	5	0	2	3	5
4A1C_3	5S_rRNA links to Rfam database...	0.72	0.59	0.88	22	2738	4	0	3	1	15
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.20	5	4491	24	5	15	4	15
4AOB_A	SAM links to Rfam database...	0.87	0.76	1.00	22	1415	3	0	0	3	7
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.57	0.33	1.00	5	491	0	0	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.19	0.17	0.25	4	1186	12	1	11	0	20

Total Scores
MCC	0.046
Average MCC ± 95% Confidence Intervals	0.018 ± 0.027
Sensitivity	0.009
Positive Predictive Value	0.273
Nr of predictions	14

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_C	5_8S_rRNA links to Rfam database...	0.15	0.07	0.33	2	5368	24	0	4	20	27
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.