CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Murlet(20)		Murlet(seed)
MCC	0.619	>	0.564
Average MCC ± 95% Confidence Intervals	0.594 ± 0.122	>	0.561 ± 0.072
Sensitivity	0.527	>	0.366
Positive Predictive Value	0.734	<	0.876
Total TP	213	>	148
Total TN	38297	<	38418
Total FP	105	>	28
Total FP CONTRA	21	>	4
Total FP INCONS	56	>	17
Total FP COMP	28	>	7
Total FN	191	<	256
P-value	2.39162260866e-08

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

Total Scores
MCC	0.619
Average MCC ± 95% Confidence Intervals	0.594 ± 0.122
Sensitivity	0.527
Positive Predictive Value	0.734
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3GX2_A	SAM links to Rfam database...	0.73	0.54	1.00	15	1434	1	0	0	1	13
3IVN_B	Purine links to Rfam database...	0.80	0.65	1.00	15	888	0	0	0	0	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.35	0.33	0.38	5	2729	13	2	6	5	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.54	0.53	0.56	10	4743	13	2	6	5	9
3LA5_A	Purine links to Rfam database...	0.80	0.64	1.00	16	938	0	0	0	0	9
3NPB_A	SAM links to Rfam database...	0.65	0.43	1.00	16	2262	2	0	0	2	21
3O58_3	5_8S_rRNA links to Rfam database...	0.37	0.32	0.44	7	4748	13	4	5	4	15
3PDR_A	ykoK links to Rfam database...	0.84	0.76	0.93	38	4799	3	1	2	0	12
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
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	0.564
Average MCC ± 95% Confidence Intervals	0.561 ± 0.072
Sensitivity	0.366
Positive Predictive Value	0.876
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3GX2_A	SAM links to Rfam database...	0.70	0.50	1.00	14	1435	1	0	0	1	14
3IVN_B	Purine links to Rfam database...	0.62	0.52	0.75	12	887	4	2	2	0	11
3J3E_8	5_8S_rRNA links to Rfam database...	0.36	0.13	1.00	2	2740	2	0	0	2	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.61	0.37	1.00	7	4754	0	0	0	0	12
3LA5_A	Purine links to Rfam database...	0.67	0.56	0.82	14	937	3	1	2	0	11
3NPB_A	SAM links to Rfam database...	0.59	0.35	1.00	13	2265	2	0	0	2	24
3O58_3	5_8S_rRNA links to Rfam database...	0.52	0.27	1.00	6	4758	1	0	0	1	16
3PDR_A	ykoK links to Rfam database...	0.53	0.28	1.00	14	4826	0	0	0	0	36
3RKF_A	Purine links to Rfam database...	0.62	0.50	0.80	12	851	3	1	2	0	12
3SD1_A	THF links to Rfam database...	0.56	0.38	0.85	11	1520	2	0	2	0	18
3ZEX_C	5_8S_rRNA links to Rfam database...	0.49	0.24	1.00	7	5367	0	0	0	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.59	0.35	1.00	7	4509	0	0	0	0	13
4AOB_A	SAM links to Rfam database...	0.69	0.48	1.00	14	1423	1	0	0	1	15
4ENB_A	crcB links to Rfam database...	0.63	0.40	1.00	6	466	0	0	0	0	9
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9
4FRG_B	AdoCbl-variant links to Rfam database...	0.17	0.13	0.25	3	1190	9	0	9	0	21

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