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)		Vsfold4
MCC	0.776	>	0.595
Average MCC ± 95% Confidence Intervals	0.769 ± 0.071	>	0.653 ± 0.103
Sensitivity	0.736	>	0.595
Positive Predictive Value	0.824	>	0.603
Total TP	790	>	639
Total TN	110252	>	110152
Total FP	346	<	534
Total FP CONTRA	66	<	128
Total FP INCONS	103	<	292
Total FP COMP	177	>	114
Total FN	284	<	435
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of MXScarna(seed) and Vsfold4. 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 Vsfold4).
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 Vsfold4).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(seed) and Vsfold4. 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 Vsfold4).

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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 Vsfold4 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold4

Total Base Pair Counts
Total TP	639
Total TN	110152
Total FP	534
Total FP CONTRA	128
Total FP INCONS	292
Total FP COMP	114
Total FN	435

Total Scores
MCC	0.595
Average MCC ± 95% Confidence Intervals	0.653 ± 0.103
Sensitivity	0.595
Positive Predictive Value	0.603
Nr of predictions	44

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2. Individual counts for Vsfold4 [ 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...	0.67	0.57	0.81	13	747	3	0	3	0	10
2L1F_B	Gammaretro_CES links to Rfam database...	0.69	0.58	0.82	14	774	3	0	3	0	10
2L94_A	HIV_FE links to Rfam database...	0.94	0.89	1.00	16	341	1	0	0	1	2
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	515	13	0	13	0	18
2WRQ_Y	tRNA links to Rfam database...	0.94	0.89	1.00	8	1144	13	0	0	13	1
2WWQ_V	tRNA links to Rfam database...	0.78	0.74	0.82	14	1187	4	1	2	1	5
2XKV_B	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	1808	27	13	14	0	11
2XQD_Y	tRNA links to Rfam database...	0.95	0.90	1.00	19	1110	1	0	0	1	2
2XXA_G	Bacteria_small_SRP links to Rfam database...	-0.02	0.00	0.00	0	2016	29	1	28	0	35
2ZZM_B	tRNA links to Rfam database...	0.18	0.20	0.19	3	1342	22	4	9	9	12
2ZZN_D	tRNA links to Rfam database...	0.95	0.95	0.95	21	962	1	1	0	0	1
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...	0.95	0.90	1.00	27	1473	0	0	0	0	3
3AKZ_H	tRNA links to Rfam database...	0.77	0.75	0.79	15	1108	6	2	2	2	5
3AMU_B	tRNA links to Rfam database...	0.73	0.74	0.74	14	1138	8	0	5	3	5
3GX2_A	SAM links to Rfam database...	0.60	0.57	0.64	16	1424	10	0	9	1	12
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...	0.27	0.35	0.21	18	22353	80	40	29	11	33
3IZ4_A	tmRNA links to Rfam database...	0.39	0.39	0.39	37	25441	63	15	43	5	58
3IZF_C	5S_rRNA links to Rfam database...	0.85	0.83	0.88	29	2607	6	0	4	2	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...	-0.02	0.00	0.00	0	1092	19	4	15	0	20
3JYX_3	5S_rRNA links to Rfam database...	0.64	0.67	0.63	10	2362	16	5	1	10	5
3JYX_4	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	3	4736	33	9	8	16	9
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...	0.66	0.59	0.73	22	2248	10	0	8	2	15
3O58_3	5_8S_rRNA links to Rfam database...	0.12	0.14	0.11	3	4737	35	8	16	11	19
3O58_2	5S_rRNA links to Rfam database...	0.53	0.52	0.55	16	2725	16	3	10	3	15
3PDR_A	ykoK links to Rfam database...	0.69	0.64	0.74	32	4797	13	3	8	2	18
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...	0.23	0.24	0.24	7	1504	22	5	17	0	22
3UZL_B	tRNA links to Rfam database...	0.66	0.69	0.65	11	1276	10	3	3	4	5
4A1C_3	5S_rRNA links to Rfam database...	0.29	0.30	0.31	11	2727	26	4	21	1	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.36	0.40	0.33	8	4492	28	4	12	12	12
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.77	0.60	1.00	9	487	0	0	0	0	6

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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 Vsfold4 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold4

2. Individual counts for Vsfold4 [ download as .csv ]