CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PknotsRG		RNASampler(seed)
MCC	0.639	>	0.635
Average MCC ± 95% Confidence Intervals	0.706 ± 0.129	>	0.663 ± 0.127
Sensitivity	0.588	>	0.484
Positive Predictive Value	0.699	<	0.837
Total TP	318	>	262
Total TN	79853	<	79995
Total FP	187	>	73
Total FP CONTRA	16	>	5
Total FP INCONS	121	>	46
Total FP COMP	50	>	22
Total FN	223	<	279
P-value	0.000481443120598

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

Total Scores
MCC	0.639
Average MCC ± 95% Confidence Intervals	0.706 ± 0.129
Sensitivity	0.588
Positive Predictive Value	0.699
Nr of predictions	19

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...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KE6_A	K10_TLS links to Rfam database...	0.86	0.84	0.89	16	1110	3	0	2	1	3
2KUR_A	K10_TLS links to Rfam database...	0.85	0.81	0.89	17	1109	2	0	2	0	4
2KUU_A	K10_TLS links to Rfam database...	0.82	0.76	0.89	16	1110	3	0	2	1	5
2KUV_A	K10_TLS links to Rfam database...	0.83	0.77	0.89	17	1109	2	0	2	0	5
2KUW_A	K10_TLS links to Rfam database...	0.90	0.86	0.95	18	1109	1	0	1	0	3
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	0.63	0.55	0.73	11	1525	4	1	3	0	9
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.32	10	12215	33	5	16	12	23
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	34	2	21	11	23
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.61	0.50	0.75	21	3888	7	1	6	0	21
3W3S_B	tRNA-Sec links to Rfam database...	0.58	0.53	0.66	21	4721	12	1	10	1	19
3ZEX_C	5_8S_rRNA links to Rfam database...	0.24	0.21	0.28	11	14157	43	1	27	15	41
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.13	5	11742	43	5	29	9	28

Total Scores
MCC	0.635
Average MCC ± 95% Confidence Intervals	0.663 ± 0.127
Sensitivity	0.484
Positive Predictive Value	0.837
Nr of predictions	19

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...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KE6_A	K10_TLS links to Rfam database...	0.92	0.84	1.00	16	1112	1	0	0	1	3
2KUR_A	K10_TLS links to Rfam database...	0.90	0.81	1.00	17	1111	0	0	0	0	4
2KUU_A	K10_TLS links to Rfam database...	0.87	0.76	1.00	16	1112	1	0	0	1	5
2KUV_A	K10_TLS links to Rfam database...	0.88	0.77	1.00	17	1111	0	0	0	0	5
2KUW_A	K10_TLS links to Rfam database...	0.90	0.81	1.00	17	1111	0	0	0	0	4
2L1F_A	Gammaretro_CES links to Rfam database...	0.81	0.67	1.00	16	2064	0	0	0	0	8
2L1F_B	Gammaretro_CES links to Rfam database...	0.82	0.68	1.00	17	2128	0	0	0	0	8
2L94_A	HIV_FE links to Rfam database...	0.71	0.55	0.92	11	978	1	0	1	0	9
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1530	10	0	10	0	20
3A3A_A	tRNA-Sec links to Rfam database...	0.70	0.49	1.00	18	3637	0	0	0	0	19
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.30	0.50	10	12226	13	2	8	3	23
3O58_3	5_8S_rRNA links to Rfam database...	0.45	0.34	0.60	12	12383	12	2	6	4	23
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.60	0.38	0.94	16	3899	1	0	1	0	26
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.30	1.00	12	4741	1	0	0	1	28
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.19	0.53	10	14177	13	1	8	4	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.31	0.24	0.40	8	11761	20	0	12	8	25

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