CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ProbKnot		Vsfold5
MCC	0.619	>	0.492
Average MCC ± 95% Confidence Intervals	0.681 ± 0.064	>	0.593 ± 0.073
Sensitivity	0.566	>	0.427
Positive Predictive Value	0.681	>	0.572
Total TP	1286	>	971
Total TN	376752	<	376944
Total FP	697	<	786
Total FP CONTRA	86	<	91
Total FP INCONS	517	<	635
Total FP COMP	94	>	60
Total FN	986	<	1301
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of ProbKnot and Vsfold5. 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 ProbKnot and Vsfold5).
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 ProbKnot and Vsfold5).
Comparison of average Matthews Correlation Coefficients (MCCs) for ProbKnot and Vsfold5. 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 ProbKnot and Vsfold5).

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Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	1286
Total TN	376752
Total FP	697
Total FP CONTRA	86
Total FP INCONS	517
Total FP COMP	94
Total FN	986

Total Scores
MCC	0.619
Average MCC ± 95% Confidence Intervals	0.681 ± 0.064
Sensitivity	0.566
Positive Predictive Value	0.681
Nr of predictions	83

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.69	0.60	0.80	24	5121	11	2	4	5	16
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2KXM_A	-	0.78	0.70	0.88	7	343	1	0	1	0	3
2KZL_A	-	0.83	0.74	0.93	14	1470	1	0	1	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L2K_A	-	0.94	0.89	1.00	17	844	0	0	0	0	2
2L3C_B	-	0.91	0.82	1.00	14	547	0	0	0	0	3
2L3E_A	-	0.96	0.92	1.00	12	583	1	0	0	1	1
2L3J_B	mir-2985-2 links to Rfam database...	0.94	0.88	1.00	30	2455	0	0	0	0	4
2L5Z_A	-	0.86	0.75	1.00	9	316	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LA5_A	-	0.45	0.32	0.67	6	621	3	0	3	0	13
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.85	0.77	0.94	30	6073	4	0	2	2	9
2LWK_A	-	0.88	0.85	0.92	11	484	1	0	1	0	2
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	24	0	9	15	10
2XQD_Y	tRNA links to Rfam database...	0.90	0.81	1.00	22	2828	1	0	0	1	5
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.26	0.24	0.29	10	5116	25	1	24	0	32
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.65	0.63	0.68	15	2256	8	1	6	1	9
2YIE_X	-	0.34	0.33	0.36	4	1367	7	2	5	0	8
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
3AKZ_H	tRNA links to Rfam database...	0.73	0.75	0.72	21	2672	8	4	4	0	7
3AM1_B	-	0.74	0.71	0.78	25	3208	7	1	6	0	10
3AMU_B	tRNA links to Rfam database...	0.65	0.59	0.73	16	2981	8	0	6	2	11
3IYQ_A	tmRNA links to Rfam database...	0.28	0.31	0.26	29	60616	85	22	59	4	65
3IZ4_A	tmRNA links to Rfam database...	0.52	0.46	0.60	61	70774	46	6	35	5	71
3IZF_C	5S_rRNA links to Rfam database...	0.72	0.61	0.85	33	6864	6	0	6	0	21
3J0L_h	-	0.77	0.65	0.90	28	6074	3	0	3	0	15
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.55	0.50	0.62	8	1115	5	2	3	0	8
3J0L_2	-	0.27	0.27	0.28	9	6184	26	2	21	3	24
3J0L_g	-	-0.01	0.00	0.00	0	458	7	2	5	0	4
3J0L_1	-	0.76	0.63	0.92	12	1212	3	0	1	2	7
3J16_L	tRNA links to Rfam database...	0.35	0.33	0.38	10	2749	16	1	15	0	20
3J20_1	tRNA links to Rfam database...	0.71	0.70	0.73	16	2904	7	0	6	1	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	0.52	0.70	33	10249	15	0	14	1	30
3J2L_3	5S_rRNA links to Rfam database...	0.60	0.49	0.74	26	7840	11	0	9	2	27
3NDB_M	-	0.77	0.69	0.88	42	9132	7	0	6	1	19
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NMU_E	-	-0.01	0.00	0.00	0	552	11	2	7	2	6
3NPB_A	SAM links to Rfam database...	0.72	0.61	0.85	28	6988	8	1	4	3	18
3O58_2	5S_rRNA links to Rfam database...	0.76	0.76	0.76	29	7222	10	3	6	1	9
3O58_3	5_8S_rRNA links to Rfam database...	0.31	0.34	0.29	12	12362	41	4	25	12	23
3OVB_D	-	1.00	1.00	1.00	11	584	2	0	0	2	0
3OVS_D	-	0.92	0.92	0.92	12	548	1	0	1	0	1
3P22_G	-	0.96	0.92	1.00	11	730	1	0	0	1	1
3PDR_A	ykoK links to Rfam database...	0.74	0.64	0.85	46	12826	10	1	7	2	26
3R4F_A	-	0.96	0.92	1.00	23	2122	0	0	0	0	2
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
3RKF_A	Purine links to Rfam database...	0.73	0.59	0.91	20	2189	2	1	1	0	14
3SD1_A	THF links to Rfam database...	0.55	0.48	0.65	20	3885	11	2	9	0	22
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
3SN2_B	IRE_II links to Rfam database...	1.00	1.00	1.00	12	394	0	0	0	0	0
3TRZ_Z	-	0.91	0.83	1.00	5	205	2	0	0	2	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.45	0.35	0.59	13	3138	9	1	8	0	24
3UZL_B	tRNA links to Rfam database...	0.73	0.62	0.85	23	3543	4	0	4	0	14
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.89	0.80	1.00	32	4721	1	0	0	1	8
3ZEX_D	5S_rRNA links to Rfam database...	0.77	0.67	0.89	33	6984	4	0	4	0	16
3ZEX_E	-	0.00	0.00	0.00	0	21886	61	2	57	2	77
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.12	5	11738	49	7	31	11	28
4A1C_3	5S_rRNA links to Rfam database...	0.73	0.61	0.87	33	7102	6	1	4	1	21
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ATO_G	-	0.32	0.30	0.38	3	520	5	1	4	0	7
4ENB_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1263	1	1	0	0	8
4ENC_A	crcB links to Rfam database...	0.45	0.42	0.50	8	1310	8	1	7	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.37	0.31	0.45	10	3464	12	3	9	0	22
4FRN_A	AdoCbl-variant links to Rfam database...	0.44	0.36	0.54	13	5127	11	2	9	0	23

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Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

Total Base Pair Counts
Total TP	971
Total TN	376944
Total FP	786
Total FP CONTRA	91
Total FP INCONS	635
Total FP COMP	60
Total FN	1301

Total Scores
MCC	0.492
Average MCC ± 95% Confidence Intervals	0.593 ± 0.073
Sensitivity	0.427
Positive Predictive Value	0.572
Nr of predictions	83

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2. Individual counts for Vsfold5 [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.57	0.50	0.65	20	5120	11	5	6	0	20
2KX8_A	7SK links to Rfam database...	0.91	0.83	1.00	15	846	0	0	0	0	3
2KXM_A	-	0.70	0.50	1.00	5	346	0	0	0	0	5
2KZL_A	-	0.86	0.74	1.00	14	1471	0	0	0	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.70	0.60	0.83	15	2127	3	0	3	0	10
2L1F_A	Gammaretro_CES links to Rfam database...	0.69	0.58	0.82	14	2063	3	0	3	0	10
2L2K_A	-	0.89	0.79	1.00	15	846	0	0	0	0	4
2L3C_B	-	0.91	0.82	1.00	14	547	0	0	0	0	3
2L3E_A	-	0.96	0.92	1.00	12	583	1	0	0	1	1
2L3J_B	mir-2985-2 links to Rfam database...	0.87	0.76	1.00	26	2459	0	0	0	0	8
2L5Z_A	-	0.60	0.50	0.75	6	317	2	0	2	0	6
2L94_A	HIV_FE links to Rfam database...	0.95	0.90	1.00	18	972	0	0	0	0	2
2LA5_A	-	-0.02	0.00	0.00	0	623	7	0	7	0	19
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1527	13	0	13	0	20
2LDL_A	-	0.85	0.73	1.00	8	343	1	0	0	1	3
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	0.89	0.80	1.00	8	268	0	0	0	0	2
2LKR_A	-	0.27	0.23	0.32	9	6077	19	2	17	0	30
2LWK_A	-	0.83	0.77	0.91	10	485	1	0	1	0	3
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2XKV_B	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	4528	32	12	20	0	20
2XQD_Y	tRNA links to Rfam database...	0.86	0.74	1.00	20	2830	0	0	0	0	7
2XXA_G	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	5120	31	2	29	0	42
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.61	0.54	0.68	13	2259	7	1	5	1	11
2YIE_X	-	0.30	0.33	0.29	4	1364	10	2	8	0	8
2YIE_Z	-	-0.01	0.00	0.00	0	1529	11	3	8	0	12
3AKZ_H	tRNA links to Rfam database...	0.84	0.71	1.00	20	2681	0	0	0	0	8
3AM1_B	-	0.78	0.71	0.86	25	3211	4	1	3	0	10
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3IYQ_A	tmRNA links to Rfam database...	0.33	0.31	0.35	29	60642	61	15	40	6	65
3IZ4_A	tmRNA links to Rfam database...	0.29	0.24	0.36	32	70787	62	8	49	5	100
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.56	0.88	30	6869	4	0	4	0	24
3J0L_h	-	0.18	0.14	0.24	6	6080	19	1	18	0	37
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_8	-	0.70	0.50	1.00	4	186	0	0	0	0	4
3J0L_a	-	0.39	0.31	0.50	5	1118	5	2	3	0	11
3J0L_2	-	0.35	0.33	0.37	11	6186	21	3	16	2	22
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_1	-	0.27	0.21	0.36	4	1214	7	1	6	0	15
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...	0.71	0.70	0.73	16	2904	6	0	6	0	7
3J20_0	tRNA links to Rfam database...	0.67	0.57	0.81	17	2829	5	1	3	1	13
3J2C_O	-	0.30	0.24	0.39	15	10258	24	0	23	1	48
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.45	0.71	24	7841	13	1	9	3	29
3NDB_M	-	0.06	0.05	0.08	3	9144	33	1	32	0	58
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NMU_E	-	0.20	0.17	0.25	1	557	5	0	3	2	5
3NPB_A	SAM links to Rfam database...	0.57	0.46	0.72	21	6992	9	1	7	1	25
3O58_2	5S_rRNA links to Rfam database...	0.45	0.42	0.48	16	7227	19	3	14	2	22
3O58_3	5_8S_rRNA links to Rfam database...	0.39	0.37	0.41	13	12371	28	7	12	9	22
3OVB_D	-	1.00	1.00	1.00	11	584	1	0	0	1	0
3OVS_D	-	0.96	0.92	1.00	12	549	0	0	0	0	1
3P22_G	-	0.96	0.92	1.00	11	730	0	0	0	0	1
3PDR_A	ykoK links to Rfam database...	0.57	0.44	0.74	32	12837	13	0	11	2	40
3R4F_A	-	0.94	0.88	1.00	22	2123	0	0	0	0	3
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
3RKF_A	Purine links to Rfam database...	0.75	0.65	0.88	22	2186	3	0	3	0	12
3SD1_A	THF links to Rfam database...	0.11	0.10	0.15	4	3890	22	0	22	0	38
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3TRZ_Z	-	0.91	0.83	1.00	5	205	1	0	0	1	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.16	0.14	0.20	5	3545	20	1	19	0	32
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.76	0.70	0.82	28	4719	7	1	5	1	12
3ZEX_D	5S_rRNA links to Rfam database...	0.08	0.06	0.11	3	6994	24	0	24	0	46
3ZEX_E	-	0.07	0.06	0.08	5	21886	54	5	49	0	72
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.24	0.24	8	11748	37	3	22	12	25
4A1C_3	5S_rRNA links to Rfam database...	0.26	0.22	0.32	12	7103	25	2	23	0	42
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.18	0.14	0.25	6	4347	19	1	17	1	36
4ATO_G	-	0.56	0.60	0.55	6	517	5	1	4	0	4
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.56	0.47	0.68	15	3464	7	1	6	0	17
4FRN_A	AdoCbl-variant links to Rfam database...	0.13	0.11	0.17	4	5128	19	2	17	0	32

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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 ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

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

Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

2. Individual counts for Vsfold5 [ download as .csv ]