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	0.667	>	0.555
Average MCC ± 95% Confidence Intervals	0.663 ± 0.057	>	0.616 ± 0.072
Sensitivity	0.560	>	0.495
Positive Predictive Value	0.794	>	0.625
Total TP	1379	>	1218
Total TN	1460602	>	1460388
Total FP	462	<	838
Total FP CONTRA	59	<	79
Total FP INCONS	298	<	653
Total FP COMP	105	<	106
Total FN	1082	<	1243
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	1379
Total TN	1460602
Total FP	462
Total FP CONTRA	59
Total FP INCONS	298
Total FP COMP	105
Total FN	1082

Total Scores
MCC	0.667
Average MCC ± 95% Confidence Intervals	0.663 ± 0.057
Sensitivity	0.560
Positive Predictive Value	0.794
Nr of predictions	53

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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
2KE6_A	K10_TLS links to Rfam database...	0.89	0.84	0.94	16	1111	2	0	1	1	3
2KUR_A	K10_TLS links to Rfam database...	0.87	0.81	0.94	17	1110	1	0	1	0	4
2KUU_A	K10_TLS links to Rfam database...	0.84	0.76	0.94	16	1111	2	0	1	1	5
2KUV_A	K10_TLS links to Rfam database...	0.85	0.77	0.94	17	1110	1	0	1	0	5
2KUW_A	K10_TLS links to Rfam database...	0.76	0.67	0.88	14	1112	2	0	2	0	7
2KX8_A	7SK links to Rfam database...	-0.01	0.00	0.00	0	859	2	0	2	0	18
2L1F_A	Gammaretro_CES links to Rfam database...	0.91	0.88	0.95	21	2058	1	0	1	0	3
2L1F_B	Gammaretro_CES links to Rfam database...	0.96	0.92	1.00	23	2122	0	0	0	0	2
2L94_A	HIV_FE links to Rfam database...	0.57	0.55	0.61	11	972	7	0	7	0	9
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
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.59	0.55	0.65	11	4543	18	0	6	12	9
2XQD_Y	tRNA links to Rfam database...	0.77	0.67	0.90	18	2830	2	0	2	0	9
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.67	0.57	0.80	24	5121	7	0	6	1	18
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_2	SSU_rRNA_archaea links to Rfam database...	0.67	0.58	0.77	366	1116289	118	14	96	8	267
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
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_3	5_8S_rRNA links to Rfam database...	0.45	0.34	0.60	12	12383	19	2	6	11	23
3O58_2	5S_rRNA links to Rfam database...	0.79	0.79	0.79	30	7222	10	4	4	2	8
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
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
4A1C_3	5S_rRNA links to Rfam database...	0.75	0.65	0.88	35	7100	5	1	4	0	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.35	0.24	0.50	8	11765	20	1	7	12	25
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

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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	1218
Total TN	1460388
Total FP	838
Total FP CONTRA	79
Total FP INCONS	653
Total FP COMP	106
Total FN	1243

Total Scores
MCC	0.555
Average MCC ± 95% Confidence Intervals	0.616 ± 0.072
Sensitivity	0.495
Positive Predictive Value	0.625
Nr of predictions	53

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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
2KE6_A	K10_TLS links to Rfam database...	0.97	0.95	1.00	18	1110	1	0	0	1	1
2KUR_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
2KUU_A	K10_TLS links to Rfam database...	0.92	0.86	1.00	18	1110	1	0	0	1	3
2KUV_A	K10_TLS links to Rfam database...	0.93	0.86	1.00	19	1109	0	0	0	0	3
2KUW_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
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
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.47	0.45	0.50	9	4542	21	0	9	12	11
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.34	0.31	0.39	13	5118	20	1	19	0	29
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_0	tRNA links to Rfam database...	0.43	0.40	0.48	12	2825	14	0	13	1	18
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.47	0.41	0.53	260	1116278	230	15	212	3	373
3J20_1	tRNA links to Rfam database...	0.73	0.70	0.76	16	2905	5	0	5	0	7
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
3JYV_7	tRNA links to Rfam database...	0.22	0.19	0.29	6	2829	15	0	15	0	26
3JYX_4	5_8S_rRNA links to Rfam database...	0.32	0.30	0.34	10	12217	31	3	16	12	23
3JYX_3	5S_rRNA links to Rfam database...	0.62	0.63	0.61	17	6300	22	1	10	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...	0.78	0.65	0.94	30	6989	5	0	2	3	16
3O58_3	5_8S_rRNA links to Rfam database...	0.35	0.34	0.35	12	12369	33	1	21	11	23
3O58_2	5S_rRNA links to Rfam database...	0.71	0.71	0.71	27	7222	12	4	7	1	11
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
3W3S_B	tRNA-Sec links to Rfam database...	0.56	0.50	0.63	20	4721	13	1	11	1	20
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...	0.77	0.65	0.91	32	6986	3	0	3	0	17
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	42	5	26	11	28
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

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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 ]