CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		Murlet(seed)
MCC	0.788	>	0.624
Average MCC ± 95% Confidence Intervals	0.823 ± 0.116	>	0.615 ± 0.093
Sensitivity	0.794	>	0.463
Positive Predictive Value	0.789	<	0.853
Total TP	340	>	198
Total TN	27526	<	27725
Total FP	158	>	43
Total FP CONTRA	28	>	4
Total FP INCONS	63	>	30
Total FP COMP	67	>	9
Total FN	88	<	230
P-value	5.19332990918e-08

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

Total Scores
MCC	0.788
Average MCC ± 95% Confidence Intervals	0.823 ± 0.116
Sensitivity	0.794
Positive Predictive Value	0.789
Nr of predictions	20

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
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	449	1	0	0	1	0
2KUR_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	448	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	429	1	0	0	1	0
2KUV_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	420	0	0	0	0	0
2KUW_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	452	1	0	0	1	0
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	1.00	0.96	23	739	1	0	1	0	0
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	1.00	0.96	24	766	1	0	1	0	0
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	6	0	5	1	7
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.35	0.34	0.38	12	2013	21	1	19	1	23
3A3A_A	tRNA-Sec links to Rfam database...	0.93	0.87	1.00	26	1474	0	0	0	0	4
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	35	10	2	23	2
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NPB_A	SAM links to Rfam database...	0.82	0.73	0.93	27	2249	6	0	2	4	10
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4

Total Scores
MCC	0.624
Average MCC ± 95% Confidence Intervals	0.615 ± 0.093
Sensitivity	0.463
Positive Predictive Value	0.853
Nr of predictions	20

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
2KE6_A	K10_TLS links to Rfam database...	0.67	0.56	0.83	10	455	2	0	2	0	8
2KUR_A	K10_TLS links to Rfam database...	0.65	0.53	0.83	10	455	2	0	2	0	9
2KUU_A	K10_TLS links to Rfam database...	0.67	0.56	0.83	10	435	2	0	2	0	8
2KUV_A	K10_TLS links to Rfam database...	0.91	0.84	1.00	16	423	0	0	0	0	3
2KUW_A	K10_TLS links to Rfam database...	0.88	0.83	0.94	15	454	2	0	1	1	3
2L1F_A	Gammaretro_CES links to Rfam database...	0.83	0.78	0.90	18	743	2	0	2	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.82	0.75	0.90	18	771	2	0	2	0	6
2L94_A	HIV_FE links to Rfam database...	0.57	0.39	0.88	7	349	2	0	1	1	11
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	516	12	0	12	0	18
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.41	0.17	1.00	6	2039	0	0	0	0	29
3A3A_A	tRNA-Sec links to Rfam database...	0.63	0.40	1.00	12	1488	0	0	0	0	18
3IVN_B	Purine links to Rfam database...	0.62	0.52	0.75	12	887	4	2	2	0	11
3JYX_4	5_8S_rRNA links to Rfam database...	0.50	0.25	1.00	3	4753	4	0	0	4	9
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
3RKF_A	Purine links to Rfam database...	0.62	0.50	0.80	12	851	3	1	2	0	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.59	0.35	1.00	7	4509	0	0	0	0	13
4ENB_A	crcB links to Rfam database...	0.63	0.40	1.00	6	466	0	0	0	0	9

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