CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Sfold		HotKnots
MCC	0.552	>	0.535
Average MCC ± 95% Confidence Intervals	0.533 ± 0.055	<	0.533 ± 0.058
Sensitivity	0.459	<	0.474
Positive Predictive Value	0.669	>	0.610
Total TP	1412	<	1457
Total TN	611315	>	611038
Total FP	820	<	1042
Total FP CONTRA	86	<	127
Total FP INCONS	614	<	805
Total FP COMP	120	>	110
Total FN	1665	>	1620
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Sfold and HotKnots. 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 Sfold and HotKnots).
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 Sfold and HotKnots).
Comparison of average Matthews Correlation Coefficients (MCCs) for Sfold and HotKnots. 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 Sfold and HotKnots).

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Performance of Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP	1412
Total TN	611315
Total FP	820
Total FP CONTRA	86
Total FP INCONS	614
Total FP COMP	120
Total FN	1665

Total Scores
MCC	0.552
Average MCC ± 95% Confidence Intervals	0.533 ± 0.055
Sensitivity	0.459
Positive Predictive Value	0.669
Nr of predictions	82

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2. Individual counts for Sfold [ 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
2KFC_A	-	-0.02	0.00	0.00	0	623	7	0	7	0	20
2KRL_A	-	0.76	0.60	0.96	24	5126	5	0	1	4	16
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LA5_A	-	0.39	0.26	0.63	5	622	3	1	2	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.45	0.35	0.58	7	1528	5	0	5	0	13
2LKR_A	-	0.89	0.79	1.00	31	6074	1	0	0	1	8
2M58_A	-	0.29	0.18	0.50	3	1647	3	1	2	0	14
2RP0_A	-	0.64	0.42	1.00	5	346	0	0	0	0	7
2WRQ_Y	tRNA links to Rfam database...	0.53	0.53	0.53	9	2833	13	5	3	5	8
2WW9_D	-	0.29	0.12	0.75	3	1949	1	0	1	0	23
2WW9_F	-	0.69	0.70	0.70	7	290	3	0	3	0	3
2WW9_E	-	0.53	0.29	1.00	4	557	0	0	0	0	10
2WWQ_V	tRNA links to Rfam database...	0.80	0.68	0.95	19	2906	2	0	1	1	9
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...	0.12	0.09	0.17	3	3468	15	0	15	0	29
2ZZN_D	tRNA links to Rfam database...	0.82	0.78	0.88	21	2461	3	0	3	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
3ADB_C	-	0.62	0.55	0.70	21	4156	9	0	9	0	17
3AKZ_H	tRNA links to Rfam database...	0.44	0.39	0.50	11	2679	11	2	9	0	17
3AM1_B	-	0.69	0.63	0.76	22	3211	7	1	6	0	13
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.51	0.39	0.69	22	7349	10	1	9	0	35
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
3GX2_A	SAM links to Rfam database...	0.72	0.55	0.96	22	4348	2	0	1	1	18
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.63	0.58	0.70	19	4251	9	0	8	1	14
3IYQ_A	tmRNA links to Rfam database...	0.33	0.34	0.32	32	60627	71	19	48	4	62
3IZ4_A	tmRNA links to Rfam database...	0.52	0.42	0.65	56	70790	31	3	27	1	76
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.61	0.83	33	6863	7	0	7	0	21
3J0L_7	-	-0.01	0.00	0.00	0	1222	3	0	3	0	17
3J0L_2	-	0.36	0.33	0.39	11	6188	19	2	15	2	22
3J0L_g	-	-0.01	0.00	0.00	0	460	5	1	4	0	4
3J0L_a	-	0.51	0.50	0.53	8	1113	7	3	4	0	8
3J16_L	tRNA links to Rfam database...	0.29	0.23	0.37	7	2756	12	0	12	0	23
3J20_1	tRNA links to Rfam database...	0.73	0.70	0.76	16	2905	6	0	5	1	7
3J20_0	tRNA links to Rfam database...	0.43	0.40	0.48	12	2825	14	0	13	1	18
3J2C_O	-	0.64	0.48	0.86	30	10261	6	0	5	1	33
3J2C_M	-	0.63	0.49	0.80	102	106363	31	3	23	5	105
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
3J3D_C	tRNA links to Rfam database...	0.36	0.25	0.54	7	2762	6	0	6	0	21
3J3E_7	5S_rRNA links to Rfam database...	0.60	0.50	0.73	27	7103	10	1	9	0	27
3J3E_8	5_8S_rRNA links to Rfam database...	0.06	0.06	0.08	2	7477	32	2	22	8	31
3J3F_7	5S_rRNA links to Rfam database...	0.69	0.60	0.79	30	7222	8	1	7	0	20
3J3F_8	5_8S_rRNA links to Rfam database...	0.35	0.33	0.38	12	12214	34	3	17	14	24
3J3V_B	5S_rRNA links to Rfam database...	0.51	0.37	0.72	21	6992	8	0	8	0	36
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2834	16	0	16	0	32
3JYX_3	5S_rRNA links to Rfam database...	0.62	0.63	0.61	17	6300	19	1	10	8	10
3JYX_4	5_8S_rRNA links to Rfam database...	0.35	0.30	0.42	10	12222	23	3	11	9	23
3KTW_C	-	0.74	0.63	0.87	27	4529	5	2	2	1	16
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.81	0.69	0.95	42	9136	3	0	2	1	19
3NKB_B	-	0.64	0.54	0.78	14	1998	4	0	4	0	12
3NPB_A	SAM links to Rfam database...	0.77	0.65	0.91	30	6988	6	1	2	3	16
3O58_2	5S_rRNA links to Rfam database...	0.74	0.74	0.74	28	7222	11	3	7	1	10
3O58_3	5_8S_rRNA links to Rfam database...	0.43	0.34	0.55	12	12381	17	0	10	7	23
3PDR_A	ykoK links to Rfam database...	0.69	0.56	0.85	40	12833	9	0	7	2	32
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...	0.65	0.50	0.84	21	3891	4	1	3	0	21
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.51	0.32	0.80	12	3555	3	2	1	0	25
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...	0.57	0.53	0.64	21	4720	13	1	11	1	19
3ZEX_E	-	0.00	0.00	0.00	0	21891	56	3	51	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.74	0.63	0.86	31	6985	5	0	5	0	18
3ZEX_H	-	0.19	0.18	0.19	7	9009	29	5	24	0	31
3ZEX_G	-	0.78	0.68	0.91	50	16416	9	0	5	4	24
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.21	0.48	11	14173	26	1	11	14	41
3ZEX_F	-	0.00	0.00	0.00	0	2623	7	2	3	2	12
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	22	1	20	1	18
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11751	34	2	23	9	28
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ATO_G	-	0.31	0.10	1.00	1	527	0	0	0	0	9
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.51	0.26	1.00	5	1321	0	0	0	0	14
4FNJ_A	-	0.79	0.63	1.00	10	585	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.62	0.47	0.83	15	3468	3	1	2	0	17
4FRN_A	AdoCbl-variant links to Rfam database...	0.63	0.44	0.89	16	5133	2	2	0	0	20
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12
4JRC_A	-	0.29	0.26	0.35	6	1523	11	0	11	0	17

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Performance of HotKnots - scored lower in this pairwise comparison

1. Total counts & total scores for HotKnots

Total Base Pair Counts
Total TP	1457
Total TN	611038
Total FP	1042
Total FP CONTRA	127
Total FP INCONS	805
Total FP COMP	110
Total FN	1620

Total Scores
MCC	0.535
Average MCC ± 95% Confidence Intervals	0.533 ± 0.058
Sensitivity	0.474
Positive Predictive Value	0.610
Nr of predictions	82

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2. Individual counts for HotKnots [ 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
2KFC_A	-	-0.02	0.00	0.00	0	623	7	0	7	0	20
2KRL_A	-	0.76	0.60	0.96	24	5126	5	0	1	4	16
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LA5_A	-	0.39	0.26	0.63	5	622	3	1	2	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2LKR_A	-	0.93	0.87	1.00	34	6071	3	0	0	3	5
2M58_A	-	0.34	0.29	0.42	5	1641	7	1	6	0	12
2RP0_A	-	0.64	0.42	1.00	5	346	0	0	0	0	7
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WW9_D	-	0.14	0.12	0.19	3	1937	13	0	13	0	23
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WW9_E	-	0.53	0.29	1.00	4	557	0	0	0	0	10
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...	0.88	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...	0.82	0.78	0.88	21	2461	3	0	3	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
3ADB_C	-	0.79	0.74	0.85	28	4153	5	0	5	0	10
3AKZ_H	tRNA links to Rfam database...	0.43	0.39	0.48	11	2678	12	2	10	0	17
3AM1_B	-	0.78	0.71	0.86	25	3211	4	0	4	0	10
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.50	0.39	0.65	22	7347	12	1	11	0	35
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
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
3IWN_A	c-di-GMP-I links to Rfam database...	0.63	0.58	0.70	19	4251	9	0	8	1	14
3IYQ_A	tmRNA links to Rfam database...	0.31	0.34	0.29	32	60617	81	22	55	4	62
3IZ4_A	tmRNA links to Rfam database...	0.51	0.47	0.55	62	70763	52	10	41	1	70
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.61	0.80	33	6862	8	1	7	0	21
3J0L_7	-	0.28	0.29	0.29	5	1208	12	0	12	0	12
3J0L_2	-	0.28	0.27	0.29	9	6185	23	3	19	1	24
3J0L_g	-	-0.01	0.00	0.00	0	460	5	1	4	0	4
3J0L_a	-	0.51	0.50	0.53	8	1113	7	3	4	0	8
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	7	0	5	2	7
3J20_0	tRNA links to Rfam database...	0.45	0.40	0.52	12	2827	12	0	11	1	18
3J2C_O	-	0.60	0.49	0.74	31	10254	12	0	11	1	32
3J2C_M	-	0.61	0.49	0.76	102	106356	38	5	28	5	105
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
3J3D_C	tRNA links to Rfam database...	0.28	0.25	0.32	7	2753	15	1	14	0	21
3J3E_7	5S_rRNA links to Rfam database...	0.59	0.50	0.71	27	7102	11	1	10	0	27
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.09	0.11	3	7476	33	2	22	9	30
3J3F_7	5S_rRNA links to Rfam database...	0.73	0.64	0.84	32	7222	7	0	6	1	18
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.31	0.30	11	12209	40	3	23	14	25
3J3V_B	5S_rRNA links to Rfam database...	0.54	0.44	0.68	25	6984	12	1	11	0	32
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2828	22	1	21	0	32
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	0.33	10	12216	31	5	15	11	23
3KTW_C	-	0.73	0.63	0.84	27	4528	6	2	3	1	16
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.84	0.74	0.96	45	9133	3	0	2	1	16
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
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...	0.23	0.26	0.21	9	12360	34	10	24	0	26
3PDR_A	ykoK links to Rfam database...	0.67	0.56	0.82	40	12831	11	0	9	2	32
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
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
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...	0.55	0.50	0.61	20	4720	14	1	12	1	20
3ZEX_E	-	0.00	0.00	0.00	0	21893	54	4	48	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.78	0.67	0.92	33	6985	3	0	3	0	16
3ZEX_H	-	0.18	0.18	0.19	7	9008	30	5	25	0	31
3ZEX_G	-	0.66	0.57	0.76	42	16416	18	0	13	5	32
3ZEX_C	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	14150	46	6	40	0	52
3ZEX_F	-	0.00	0.00	0.00	0	2617	11	2	9	0	12
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	22	1	20	1	18
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	6	25	11	28
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ATO_G	-	0.61	0.70	0.54	7	515	6	2	4	0	3
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FNJ_A	-	0.79	0.63	1.00	10	585	0	0	0	0	6
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...	0.52	0.44	0.62	16	5125	10	2	8	0	20
4JF2_A	preQ1-II links to Rfam database...	0.81	0.77	0.86	24	2822	4	3	1	0	7
4JRC_A	-	0.29	0.26	0.35	6	1523	11	0	11	0	17

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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 Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

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

Performance of HotKnots - scored lower in this pairwise comparison

1. Total counts & total scores for HotKnots

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