CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(20)		RNAalifold(seed)
MCC	0.693	>	0.673
Average MCC ± 95% Confidence Intervals	0.721 ± 0.107	>	0.677 ± 0.064
Sensitivity	0.592	>	0.492
Positive Predictive Value	0.815	<	0.925
Total TP	295	>	245
Total TN	58849	<	58946
Total FP	121	>	37
Total FP CONTRA	34	>	12
Total FP INCONS	33	>	8
Total FP COMP	54	>	17
Total FN	203	<	253
P-value	1.77512146924e-08

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

Total Scores
MCC	0.693
Average MCC ± 95% Confidence Intervals	0.721 ± 0.107
Sensitivity	0.592
Positive Predictive Value	0.815
Nr of predictions	18

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	0.94	0.94	0.94	17	339	2	0	1	1	1
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	4	1831	2	0	0	2	7
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.34	0.11	1.00	4	2041	0	0	0	0	31
3GX2_A	SAM links to Rfam database...	0.88	0.79	1.00	22	1427	1	0	0	1	6
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IZ4_A	tmRNA links to Rfam database...	0.52	0.41	0.65	39	25476	26	15	6	5	56
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	26	10	2	14	2
3LA5_A	Purine links to Rfam database...	0.89	0.80	1.00	20	934	0	0	0	0	5
3NPB_A	SAM links to Rfam database...	0.75	0.57	1.00	21	2257	5	0	0	5	16
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.50	0.52	11	4743	19	5	5	9	11
3PDR_A	ykoK links to Rfam database...	0.84	0.76	0.93	38	4799	5	1	2	2	12
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.81	0.69	0.95	20	1512	1	0	1	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	30	3	13	14	15
4AOB_A	SAM links to Rfam database...	0.70	0.59	0.85	17	1417	4	0	3	1	12
4ENB_A	crcB links to Rfam database...	0.68	0.47	1.00	7	465	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	0	0	0	0	4

Total Scores
MCC	0.673
Average MCC ± 95% Confidence Intervals	0.677 ± 0.064
Sensitivity	0.492
Positive Predictive Value	0.925
Nr of predictions	18

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.54	0.30	1.00	3	171	0	0	0	0	7
2L94_A	HIV_FE links to Rfam database...	0.57	0.39	0.88	7	349	2	0	1	1	11
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.80	0.64	1.00	7	1828	2	0	0	2	4
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.50	0.26	1.00	9	2036	0	0	0	0	26
3GX2_A	SAM links to Rfam database...	0.88	0.79	1.00	22	1427	1	0	0	1	6
3IVN_B	Purine links to Rfam database...	0.71	0.65	0.79	15	884	4	2	2	0	8
3IZ4_A	tmRNA links to Rfam database...	0.46	0.26	0.81	25	25505	8	6	0	2	70
3JYX_4	5_8S_rRNA links to Rfam database...	0.76	0.58	1.00	7	4749	2	0	0	2	5
3LA5_A	Purine links to Rfam database...	0.73	0.64	0.84	16	935	3	1	2	0	9
3NPB_A	SAM links to Rfam database...	0.77	0.59	1.00	22	2256	3	0	0	3	15
3O58_3	5_8S_rRNA links to Rfam database...	0.60	0.36	1.00	8	4756	1	0	0	1	14
3PDR_A	ykoK links to Rfam database...	0.81	0.66	1.00	33	4807	1	0	0	1	17
3RKF_A	Purine links to Rfam database...	0.74	0.67	0.84	16	847	3	1	2	0	8
3SD1_A	THF links to Rfam database...	0.70	0.59	0.85	17	1513	3	2	1	0	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.50	0.25	1.00	5	4511	2	0	0	2	15
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
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

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