CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MXScarna(seed)		Contrafold
MCC	0.776	>	0.698
Average MCC ± 95% Confidence Intervals	0.769 ± 0.071	>	0.744 ± 0.086
Sensitivity	0.736	>	0.726
Positive Predictive Value	0.824	>	0.677
Total TP	790	>	780
Total TN	110252	>	110059
Total FP	346	<	522
Total FP CONTRA	66	<	147
Total FP INCONS	103	<	225
Total FP COMP	177	>	150
Total FN	284	<	294
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of MXScarna(seed) and Contrafold. 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 MXScarna(seed) and Contrafold).
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 MXScarna(seed) and Contrafold).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(seed) and Contrafold. 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 MXScarna(seed) and Contrafold).

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Performance of MXScarna(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for MXScarna(seed)

Total Base Pair Counts
Total TP	790
Total TN	110252
Total FP	346
Total FP CONTRA	66
Total FP INCONS	103
Total FP COMP	177
Total FN	284

Total Scores
MCC	0.776
Average MCC ± 95% Confidence Intervals	0.769 ± 0.071
Sensitivity	0.736
Positive Predictive Value	0.824
Nr of predictions	44

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2. Individual counts for MXScarna(seed) [ download as .csv ]

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...	0.91	0.89	0.94	16	450	2	0	1	1	2
2KUR_A	K10_TLS links to Rfam database...	0.92	0.89	0.94	17	449	1	0	1	0	2
2KUU_A	K10_TLS links to Rfam database...	0.91	0.89	0.94	16	430	2	0	1	1	2
2KUV_A	K10_TLS links to Rfam database...	0.92	0.89	0.94	17	421	1	0	1	0	2
2KUW_A	K10_TLS links to Rfam database...	0.78	0.72	0.87	13	455	3	0	2	1	5
2KX8_A	7SK links to Rfam database...	-0.01	0.00	0.00	0	369	2	0	2	0	16
2L1F_A	Gammaretro_CES links to Rfam database...	0.93	0.91	0.95	21	741	1	0	1	0	2
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	768	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.55	0.56	0.59	10	340	8	0	7	1	8
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	518	12	0	10	2	18
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	12	0	0	12	0
2WWQ_V	tRNA links to Rfam database...	0.70	0.68	0.72	13	1186	7	0	5	2	6
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.78	0.82	0.75	9	1823	20	0	3	17	2
2XQD_Y	tRNA links to Rfam database...	0.85	0.81	0.89	17	1110	3	0	2	1	4
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.74	0.69	0.80	24	2015	7	0	6	1	11
2ZZM_B	tRNA links to Rfam database...	0.81	0.67	1.00	10	1348	9	0	0	9	5
2ZZN_D	tRNA links to Rfam database...	0.95	0.91	1.00	20	964	0	0	0	0	2
3A2K_C	tRNA links to Rfam database...	0.95	0.91	1.00	20	1088	0	0	0	0	2
3A3A_A	tRNA-Sec links to Rfam database...	0.84	0.77	0.92	23	1475	4	0	2	2	7
3AKZ_H	tRNA links to Rfam database...	1.00	1.00	1.00	20	1107	1	0	0	1	0
3AMU_B	tRNA links to Rfam database...	0.97	0.95	1.00	18	1139	2	0	0	2	1
3GX2_A	SAM links to Rfam database...	0.83	0.82	0.85	23	1422	7	2	2	3	5
3IVN_B	Purine links to Rfam database...	0.69	0.57	0.87	13	888	2	2	0	0	10
3IYQ_A	tmRNA links to Rfam database...	0.44	0.47	0.41	24	22382	49	21	13	15	27
3IZ4_A	tmRNA links to Rfam database...	0.73	0.64	0.82	61	25462	22	12	1	9	34
3IZF_C	5S_rRNA links to Rfam database...	0.84	0.83	0.85	29	2606	11	0	5	6	6
3J16_L	tRNA links to Rfam database...	0.98	0.95	1.00	20	1139	0	0	0	0	1
3JYV_7	tRNA links to Rfam database...	0.95	0.90	1.00	18	1093	2	0	0	2	2
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	24	0	4	20	3
3JYX_4	5_8S_rRNA links to Rfam database...	0.70	0.83	0.59	10	4739	21	6	1	14	2
3LA5_A	Purine links to Rfam database...	0.82	0.72	0.95	18	935	1	1	0	0	7
3NPB_A	SAM links to Rfam database...	0.76	0.70	0.84	26	2247	10	2	3	5	11
3O58_3	5_8S_rRNA links to Rfam database...	0.54	0.50	0.58	11	4745	20	5	3	12	11
3O58_2	5S_rRNA links to Rfam database...	0.93	0.94	0.94	29	2723	11	0	2	9	2
3PDR_A	ykoK links to Rfam database...	0.87	0.88	0.86	44	4789	10	4	3	3	6
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.74	0.76	0.73	22	1503	9	4	4	1	7
3UZL_B	tRNA links to Rfam database...	0.83	0.75	0.92	12	1280	8	0	1	7	4
4A1C_3	5S_rRNA links to Rfam database...	0.92	0.92	0.92	34	2726	6	0	3	3	3
4A1C_2	5_8S_rRNA links to Rfam database...	0.45	0.40	0.50	8	4500	20	4	4	12	12
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	10	2	5	3	9
4ENB_A	crcB links to Rfam database...	0.54	0.40	0.75	6	464	2	0	2	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	1	3	0	9

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Performance of Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	780
Total TN	110059
Total FP	522
Total FP CONTRA	147
Total FP INCONS	225
Total FP COMP	150
Total FN	294

Total Scores
MCC	0.698
Average MCC ± 95% Confidence Intervals	0.744 ± 0.086
Sensitivity	0.726
Positive Predictive Value	0.677
Nr of predictions	44

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2. Individual counts for Contrafold [ download as .csv ]

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
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2L1F_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	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
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.39	0.58	7	516	5	3	2	0	11
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2WWQ_V	tRNA links to Rfam database...	1.00	1.00	1.00	19	1185	4	0	0	4	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	27	0	6	21	3
2XQD_Y	tRNA links to Rfam database...	0.85	0.86	0.86	18	1108	4	0	3	1	3
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.10	0.11	0.12	4	2012	30	2	27	1	31
2ZZM_B	tRNA links to Rfam database...	0.80	0.80	0.80	12	1343	13	0	3	10	3
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	3	2	0	1	1
3A2K_C	tRNA links to Rfam database...	0.49	0.55	0.46	12	1082	14	3	11	0	10
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3AKZ_H	tRNA links to Rfam database...	0.44	0.50	0.40	10	1102	18	6	9	3	10
3AMU_B	tRNA links to Rfam database...	0.75	0.79	0.71	15	1136	9	0	6	3	4
3GX2_A	SAM links to Rfam database...	0.93	0.89	0.96	25	1423	2	1	0	1	3
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IYQ_A	tmRNA links to Rfam database...	0.28	0.39	0.20	20	22341	95	44	35	16	31
3IZ4_A	tmRNA links to Rfam database...	0.57	0.58	0.57	55	25440	49	18	23	8	40
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	11	0	5	6	3
3J16_L	tRNA links to Rfam database...	0.55	0.57	0.55	12	1137	10	3	7	0	9
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1091	20	4	16	0	20
3JYX_3	5S_rRNA links to Rfam database...	0.33	0.47	0.24	7	2349	24	16	6	2	8
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.58	0.27	7	4730	35	13	6	16	5
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...	0.86	0.84	0.89	31	2243	9	1	3	5	6
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.36	0.29	8	4736	21	7	13	1	14
3O58_2	5S_rRNA links to Rfam database...	0.92	0.94	0.91	29	2722	10	0	3	7	2
3PDR_A	ykoK links to Rfam database...	0.83	0.86	0.80	43	4786	13	5	6	2	7
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	5	4	0	9
3UZL_B	tRNA links to Rfam database...	0.90	0.88	0.93	14	1278	8	0	1	7	2
4A1C_3	5S_rRNA links to Rfam database...	0.81	0.81	0.81	30	2726	10	0	7	3	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	33	9	13	11	15
4AOB_A	SAM links to Rfam database...	0.53	0.52	0.56	15	1410	13	3	9	1	14
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	1	0	0	1	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	1	0	0	1	4

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

Table of contents:

Overview

Performance plots

Performance of MXScarna(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for MXScarna(seed)

2. Individual counts for MXScarna(seed) [ download as .csv ]

Performance of Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

2. Individual counts for Contrafold [ download as .csv ]