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)		UNAFold
MCC	0.646	>	0.524
Average MCC ± 95% Confidence Intervals	0.619 ± 0.060	>	0.552 ± 0.068
Sensitivity	0.536	>	0.464
Positive Predictive Value	0.779	>	0.595
Total TP	1365	>	1181
Total TN	1491229	>	1490995
Total FP	496	<	922
Total FP CONTRA	67	<	88
Total FP INCONS	320	<	717
Total FP COMP	109	<	117
Total FN	1183	<	1367
P-value	3.56938820447e-08

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Performance plots

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

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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	1365
Total TN	1491229
Total FP	496
Total FP CONTRA	67
Total FP INCONS	320
Total FP COMP	109
Total FN	1183

Total Scores
MCC	0.646
Average MCC ± 95% Confidence Intervals	0.619 ± 0.060
Sensitivity	0.536
Positive Predictive Value	0.779
Nr of predictions	51

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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...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KX8_A	7SK links to Rfam database...	-0.01	0.00	0.00	0	859	2	0	2	0	18
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1530	12	0	10	2	20
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	11	5	3	3	7
2WWQ_V	tRNA links to Rfam database...	0.56	0.46	0.68	13	2907	7	0	6	1	15
2XQD_Y	tRNA links to Rfam database...	0.77	0.67	0.90	18	2830	2	0	2	0	9
2ZZM_B	tRNA links to Rfam database...	0.56	0.44	0.74	14	3467	5	4	1	0	18
2ZZN_D	tRNA links to Rfam database...	0.86	0.74	1.00	20	2465	0	0	0	0	7
3A2K_C	tRNA links to Rfam database...	0.84	0.71	1.00	20	2906	0	0	0	0	8
3A3A_A	tRNA-Sec links to Rfam database...	0.77	0.65	0.92	24	3629	3	0	2	1	13
3AKZ_H	tRNA links to Rfam database...	0.86	0.75	1.00	21	2680	0	0	0	0	7
3AMU_B	tRNA links to Rfam database...	0.84	0.70	1.00	19	2984	1	0	0	1	8
3GX2_A	SAM links to Rfam database...	0.70	0.60	0.83	24	4342	6	0	5	1	16
3IVN_B	Purine links to Rfam database...	0.65	0.45	0.93	14	2331	1	1	0	0	17
3IYQ_A	tmRNA links to Rfam database...	0.45	0.38	0.54	36	60659	37	4	27	6	58
3IZ4_A	tmRNA links to Rfam database...	0.69	0.55	0.88	72	70794	11	3	7	1	60
3IZF_C	5S_rRNA links to Rfam database...	0.67	0.57	0.79	31	6864	9	1	7	1	23
3J16_L	tRNA links to Rfam database...	0.82	0.67	1.00	20	2755	0	0	0	0	10
3J20_1	tRNA links to Rfam database...	0.93	0.87	1.00	20	2906	0	0	0	0	3
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.67	0.58	0.77	366	1116289	118	14	96	8	267
3J20_0	tRNA links to Rfam database...	0.79	0.63	1.00	19	2831	0	0	0	0	11
3J2L_3	5S_rRNA links to Rfam database...	0.60	0.49	0.74	26	7840	11	1	8	2	27
3J3E_8	5_8S_rRNA links to Rfam database...	0.16	0.09	0.27	3	7492	14	1	7	6	30
3J3E_7	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	2	5	0	22
3J3F_8	5_8S_rRNA links to Rfam database...	0.45	0.33	0.60	12	12226	18	1	7	10	24
3J3F_7	5S_rRNA links to Rfam database...	0.78	0.70	0.88	35	7220	6	2	3	1	15
3J3V_B	5S_rRNA links to Rfam database...	0.56	0.46	0.70	26	6984	11	1	10	0	31
3JYV_7	tRNA links to Rfam database...	0.79	0.63	1.00	20	2830	0	0	0	0	12
3JYX_3	5S_rRNA links to Rfam database...	0.58	0.56	0.60	15	6303	21	1	9	11	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.38	0.30	0.48	10	12225	21	3	8	10	23
3LA5_A	Purine links to Rfam database...	0.75	0.56	1.00	19	2466	0	0	0	0	15
3NPB_A	SAM links to Rfam database...	0.69	0.59	0.82	27	6988	9	2	4	3	19
3O58_2	5S_rRNA links to Rfam database...	0.79	0.79	0.79	30	7222	10	4	4	2	8
3O58_3	5_8S_rRNA links to Rfam database...	0.45	0.34	0.60	12	12383	19	2	6	11	23
3PDR_A	ykoK links to Rfam database...	0.73	0.63	0.87	45	12828	9	2	5	2	27
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.63	0.55	0.74	23	3885	8	1	7	0	19
3UZL_B	tRNA links to Rfam database...	0.66	0.49	0.90	18	3550	2	1	1	0	19
3W1K_J	tRNA-Sec links to Rfam database...	0.84	0.76	0.94	29	4155	2	1	1	0	9
3W3S_B	tRNA-Sec links to Rfam database...	0.69	0.60	0.80	24	4723	6	0	6	0	16
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.69	0.83	34	6980	7	1	6	0	15
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.19	0.53	10	14177	20	2	7	11	42
3ZND_W	tRNA links to Rfam database...	0.44	0.39	0.50	9	2985	11	0	9	2	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.35	0.24	0.50	8	11765	20	1	7	12	25
4A1C_3	5S_rRNA links to Rfam database...	0.75	0.65	0.88	35	7100	5	1	4	0	19
4AOB_A	SAM links to Rfam database...	0.66	0.55	0.79	23	4342	7	0	6	1	19
4ENB_A	crcB links to Rfam database...	0.48	0.32	0.75	6	1267	2	0	2	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	1	3	0	13
4FRG_B	AdoCbl-variant links to Rfam database...	0.41	0.31	0.56	10	3468	8	2	6	0	22
4FRN_A	AdoCbl-variant links to Rfam database...	0.62	0.53	0.73	19	5125	7	2	5	0	17
4JF2_A	preQ1-II links to Rfam database...	0.44	0.32	0.63	10	2834	6	0	6	0	21

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Performance of UNAFold - scored lower in this pairwise comparison

1. Total counts & total scores for UNAFold

Total Base Pair Counts
Total TP	1181
Total TN	1490995
Total FP	922
Total FP CONTRA	88
Total FP INCONS	717
Total FP COMP	117
Total FN	1367

Total Scores
MCC	0.524
Average MCC ± 95% Confidence Intervals	0.552 ± 0.068
Sensitivity	0.464
Positive Predictive Value	0.595
Nr of predictions	51

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2. Individual counts for UNAFold [ 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...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WWQ_V	tRNA links to Rfam database...	0.78	0.68	0.90	19	2905	3	0	2	1	9
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2ZZM_B	tRNA links to Rfam database...	0.21	0.19	0.25	6	3462	18	0	18	0	26
2ZZN_D	tRNA links to Rfam database...	0.84	0.78	0.91	21	2462	2	0	2	0	6
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
3AKZ_H	tRNA links to Rfam database...	0.43	0.39	0.48	11	2678	12	2	10	0	17
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3GX2_A	SAM links to Rfam database...	0.68	0.55	0.85	22	4345	5	0	4	1	18
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IYQ_A	tmRNA links to Rfam database...	0.31	0.33	0.28	31	60617	82	22	56	4	63
3IZ4_A	tmRNA links to Rfam database...	0.51	0.45	0.58	60	70772	50	4	40	6	72
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.61	0.80	33	6862	8	1	7	0	21
3J16_L	tRNA links to Rfam database...	0.26	0.23	0.30	7	2752	16	1	15	0	23
3J20_1	tRNA links to Rfam database...	0.73	0.70	0.76	16	2905	5	0	5	0	7
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.47	0.41	0.53	260	1116278	230	15	212	3	373
3J20_0	tRNA links to Rfam database...	0.43	0.40	0.48	12	2825	14	0	13	1	18
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.09	0.12	3	7477	32	2	21	9	30
3J3E_7	5S_rRNA links to Rfam database...	0.45	0.37	0.56	20	7104	16	1	15	0	34
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.31	0.29	11	12208	41	4	23	14	25
3J3F_7	5S_rRNA links to Rfam database...	0.73	0.62	0.86	31	7224	6	0	5	1	19
3J3V_B	5S_rRNA links to Rfam database...	0.55	0.44	0.69	25	6985	11	1	10	0	32
3JYV_7	tRNA links to Rfam database...	0.22	0.19	0.29	6	2829	15	0	15	0	26
3JYX_3	5S_rRNA links to Rfam database...	0.62	0.63	0.61	17	6300	22	1	10	11	10
3JYX_4	5_8S_rRNA links to Rfam database...	0.32	0.30	0.34	10	12217	31	3	16	12	23
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.78	0.65	0.94	30	6989	5	0	2	3	16
3O58_2	5S_rRNA links to Rfam database...	0.71	0.71	0.71	27	7222	12	4	7	1	11
3O58_3	5_8S_rRNA links to Rfam database...	0.35	0.34	0.35	12	12369	33	1	21	11	23
3PDR_A	ykoK links to Rfam database...	0.77	0.64	0.94	46	12831	5	0	3	2	26
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...	0.64	0.52	0.79	22	3888	6	1	5	0	20
3UZL_B	tRNA links to Rfam database...	0.48	0.38	0.61	14	3547	9	0	9	0	23
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
3W3S_B	tRNA-Sec links to Rfam database...	0.56	0.50	0.63	20	4721	13	1	11	1	20
3ZEX_D	5S_rRNA links to Rfam database...	0.77	0.65	0.91	32	6986	3	0	3	0	17
3ZEX_C	5_8S_rRNA links to Rfam database...	0.24	0.21	0.28	11	14157	42	1	27	14	41
3ZND_W	tRNA links to Rfam database...	0.21	0.22	0.21	5	2979	20	1	18	1	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	42	5	26	11	28
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1314	7	1	6	0	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.32	0.28	0.38	9	3462	15	0	15	0	23
4FRN_A	AdoCbl-variant links to Rfam database...	0.43	0.36	0.52	13	5126	12	2	10	0	23
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

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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 UNAFold - scored lower in this pairwise comparison

1. Total counts & total scores for UNAFold

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