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)		RNAsubopt
MCC	0.638	>	0.538
Average MCC ± 95% Confidence Intervals	0.618 ± 0.061	>	0.548 ± 0.071
Sensitivity	0.522	>	0.486
Positive Predictive Value	0.783	>	0.601
Total TP	999	>	931
Total TN	374940	>	374667
Total FP	378	<	718
Total FP CONTRA	53	<	89
Total FP INCONS	224	<	529
Total FP COMP	101	>	100
Total FN	916	<	984
P-value	3.56938820447e-08

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Performance plots

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

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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	999
Total TN	374940
Total FP	378
Total FP CONTRA	53
Total FP INCONS	224
Total FP COMP	101
Total FN	916

Total Scores
MCC	0.638
Average MCC ± 95% Confidence Intervals	0.618 ± 0.061
Sensitivity	0.522
Positive Predictive Value	0.783
Nr of predictions	50

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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_0	tRNA links to Rfam database...	0.79	0.63	1.00	19	2831	0	0	0	0	11
3J20_1	tRNA links to Rfam database...	0.93	0.87	1.00	20	2906	0	0	0	0	3
3J2L_3	5S_rRNA links to Rfam database...	0.60	0.49	0.74	26	7840	11	1	8	2	27
3J3E_7	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	2	5	0	22
3J3E_8	5_8S_rRNA links to Rfam database...	0.16	0.09	0.27	3	7492	14	1	7	6	30
3J3F_7	5S_rRNA links to Rfam database...	0.78	0.70	0.88	35	7220	6	2	3	1	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.45	0.33	0.60	12	12226	18	1	7	10	24
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_4	5_8S_rRNA links to Rfam database...	0.38	0.30	0.48	10	12225	21	3	8	10	23
3JYX_3	5S_rRNA links to Rfam database...	0.58	0.56	0.60	15	6303	21	1	9	11	12
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_C	5_8S_rRNA links to Rfam database...	0.32	0.19	0.53	10	14177	20	2	7	11	42
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.69	0.83	34	6980	7	1	6	0	15
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 RNAsubopt - scored lower in this pairwise comparison

1. Total counts & total scores for RNAsubopt

Total Base Pair Counts
Total TP	931
Total TN	374667
Total FP	718
Total FP CONTRA	89
Total FP INCONS	529
Total FP COMP	100
Total FN	984

Total Scores
MCC	0.538
Average MCC ± 95% Confidence Intervals	0.548 ± 0.071
Sensitivity	0.486
Positive Predictive Value	0.601
Nr of predictions	50

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2. Individual counts for RNAsubopt [ 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...	0.91	0.83	1.00	15	846	0	0	0	0	3
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	12	5	3	4	7
2WWQ_V	tRNA links to Rfam database...	0.76	0.68	0.86	19	2904	5	0	3	2	9
2XQD_Y	tRNA links to Rfam database...	0.75	0.67	0.86	18	2829	3	0	3	0	9
2ZZM_B	tRNA links to Rfam database...	0.23	0.22	0.26	7	3459	20	2	18	0	25
2ZZN_D	tRNA links to Rfam database...	0.48	0.44	0.52	12	2462	11	1	10	0	15
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...	0.39	0.36	0.43	10	2678	13	2	11	0	18
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...	0.44	0.38	0.54	15	4343	14	1	12	1	25
3IVN_B	Purine links to Rfam database...	0.76	0.58	1.00	18	2328	0	0	0	0	13
3IYQ_A	tmRNA links to Rfam database...	0.33	0.36	0.30	34	60614	82	17	61	4	60
3IZ4_A	tmRNA links to Rfam database...	0.51	0.47	0.56	62	70766	49	8	40	1	70
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...	0.41	0.37	0.48	11	2752	12	1	11	0	19
3J20_0	tRNA links to Rfam database...	0.43	0.40	0.48	12	2825	14	0	13	1	18
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	2	0	0	2	2
3J2L_3	5S_rRNA links to Rfam database...	0.61	0.53	0.72	28	7836	13	0	11	2	25
3J3E_7	5S_rRNA links to Rfam database...	0.59	0.50	0.69	27	7101	12	1	11	0	27
3J3E_8	5_8S_rRNA links to Rfam database...	0.16	0.15	0.18	5	7475	32	2	21	9	28
3J3F_7	5S_rRNA links to Rfam database...	0.80	0.70	0.92	35	7222	4	0	3	1	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.33	0.32	12	12209	39	4	21	14	24
3J3V_B	5S_rRNA links to Rfam database...	0.54	0.42	0.71	24	6987	10	1	9	0	33
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2829	21	0	21	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.19	0.21	0.17	7	12204	38	11	24	3	26
3JYX_3	5S_rRNA links to Rfam database...	0.63	0.63	0.63	17	6301	21	1	9	11	10
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...	0.75	0.65	0.86	30	6986	7	1	4	2	16
3O58_2	5S_rRNA links to Rfam database...	0.72	0.74	0.70	28	7220	13	4	8	1	10
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	34	2	21	11	23
3PDR_A	ykoK links to Rfam database...	0.75	0.63	0.90	45	12830	7	1	4	2	27
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
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...	0.87	0.78	0.97	31	4721	2	0	1	1	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.24	0.21	0.28	11	14157	42	1	27	14	41
3ZEX_D	5S_rRNA links to Rfam database...	0.80	0.69	0.92	34	6984	3	0	3	0	15
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.13	5	11742	43	5	29	9	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...	0.52	0.43	0.64	18	4343	11	2	8	1	24
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	0	7	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...	0.51	0.44	0.59	16	5124	11	3	8	0	20
4JF2_A	preQ1-II links to Rfam database...	0.61	0.52	0.73	16	2828	6	3	3	0	15

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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 RNAsubopt - scored lower in this pairwise comparison

1. Total counts & total scores for RNAsubopt

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