CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Contrafold		ProbKnot
MCC	0.547	>	0.536
Average MCC ± 95% Confidence Intervals	0.685 ± 0.057	>	0.661 ± 0.062
Sensitivity	0.482	>	0.480
Positive Predictive Value	0.623	>	0.601
Total TP	1868	>	1862
Total TN	2714892	>	2714788
Total FP	1242	<	1364
Total FP CONTRA	128	<	149
Total FP INCONS	1000	<	1089
Total FP COMP	114	<	126
Total FN	2011	<	2017
P-value	1.27481660653e-07

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Performance plots

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

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Performance of Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	1868
Total TN	2714892
Total FP	1242
Total FP CONTRA	128
Total FP INCONS	1000
Total FP COMP	114
Total FN	2011

Total Scores
MCC	0.547
Average MCC ± 95% Confidence Intervals	0.685 ± 0.057
Sensitivity	0.482
Positive Predictive Value	0.623
Nr of predictions	93

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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
2KXM_A	-	0.89	0.80	1.00	8	343	0	0	0	0	2
2KZL_A	-	0.75	0.74	0.78	14	1467	4	2	2	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...	0.92	0.90	0.95	18	971	1	0	1	0	2
2LA5_A	-	0.39	0.26	0.63	5	622	3	1	2	0	14
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.45	0.35	0.58	7	1528	5	2	3	0	13
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	-	0.84	0.79	0.89	31	6070	6	0	4	2	8
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.88	0.85	0.92	11	484	1	0	1	0	2
2RRC_A	-	0.83	0.70	1.00	7	224	0	0	0	0	3
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	25	0	9	16	10
2XQD_Y	tRNA links to Rfam database...	0.78	0.70	0.86	19	2828	3	0	3	0	8
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.13	0.12	0.15	5	5117	29	1	28	0	37
2Y8W_B	-	1.00	1.00	1.00	6	184	3	0	0	3	0
2Y9C_V	-	0.66	0.63	0.71	15	2257	8	1	5	2	9
2YIE_Z	-	0.43	0.42	0.45	5	1529	6	3	3	0	7
2YIE_X	-	0.73	0.67	0.80	8	1368	3	1	1	1	4
3AKZ_H	tRNA links to Rfam database...	0.39	0.39	0.41	11	2674	17	4	12	1	17
3AM1_B	-	0.68	0.63	0.73	22	3210	8	1	7	0	13
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...	0.34	0.37	0.32	35	60615	80	21	55	4	59
3IZ4_A	tmRNA links to Rfam database...	0.52	0.45	0.61	60	70777	44	4	35	5	72
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.61	0.77	33	6860	10	1	9	0	21
3J0L_g	-	0.00	0.00	0.00	0	464	1	1	0	0	4
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.50	0.44	0.58	7	1116	5	2	3	0	9
3J0L_1	-	0.73	0.58	0.92	11	1213	2	0	1	1	8
3J0L_h	-	0.75	0.65	0.88	28	6073	6	0	4	2	15
3J0L_7	-	-0.01	0.00	0.00	0	1218	7	0	7	0	17
3J0L_2	-	0.25	0.24	0.28	8	6187	26	0	21	5	25
3J16_L	tRNA links to Rfam database...	0.46	0.40	0.55	12	2753	10	1	9	0	18
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.58	0.51	0.66	321	1116277	172	10	157	5	312
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	4	0	0	4	2
3J20_0	tRNA links to Rfam database...	0.44	0.40	0.50	12	2826	13	0	12	1	18
3J2C_O	-	0.79	0.67	0.93	42	10251	4	0	3	1	21
3J2C_M	-	0.43	0.34	0.53	71	106357	66	9	54	3	136
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.49	0.65	26	7835	16	0	14	2	27
3NDB_M	-	0.81	0.72	0.92	44	9132	5	0	4	1	17
3NKB_B	-	0.54	0.50	0.59	13	1994	9	0	9	0	13
3NMU_E	-	0.71	0.50	1.00	3	558	3	0	0	3	3
3NPB_A	SAM links to Rfam database...	0.76	0.70	0.84	32	6983	8	1	5	2	14
3O58_2	5S_rRNA links to Rfam database...	0.78	0.76	0.81	29	7224	10	2	5	3	9
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.26	0.31	9	12374	20	3	17	0	26
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	1	0	0	1	1
3PDR_A	ykoK links to Rfam database...	0.69	0.60	0.80	43	12826	13	0	11	2	29
3R4F_A	-	0.79	0.76	0.83	19	2122	4	1	3	0	6
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...	0.57	0.48	0.69	20	3887	9	2	7	0	22
3SIU_F	-	0.74	0.64	0.88	7	370	1	0	1	0	4
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	-	0.59	0.46	0.77	17	3138	5	0	5	0	20
3UZL_B	tRNA links to Rfam database...	0.70	0.54	0.91	20	3548	2	0	2	0	17
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_F	-	0.00	0.00	0.00	0	2619	9	2	7	0	12
3ZEX_G	-	0.28	0.24	0.33	18	16416	41	2	35	4	56
3ZEX_E	-	0.00	0.00	0.00	0	21889	58	4	52	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.67	0.80	33	6980	8	1	7	0	16
3ZEX_B	-	0.22	0.18	0.26	100	1071996	294	23	261	10	458
3ZEX_H	-	0.17	0.18	0.17	7	9003	35	6	29	0	31
3ZEX_C	5_8S_rRNA links to Rfam database...	0.28	0.21	0.38	11	14167	22	3	15	4	41
4A1C_3	5S_rRNA links to Rfam database...	0.66	0.57	0.78	31	7100	9	1	8	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11751	33	5	20	8	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.44	0.36	0.56	15	4344	13	1	11	1	27
4ATO_G	-	0.44	0.40	0.50	4	520	4	0	4	0	6
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...	0.73	0.58	0.92	11	1314	1	1	0	0	8
4FNJ_A	-	0.79	0.63	1.00	10	585	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.68	0.56	0.82	18	3464	4	1	3	0	14
4FRN_A	AdoCbl-variant links to Rfam database...	0.65	0.56	0.77	20	5125	6	1	5	0	16
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	0	0	0

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Performance of ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	1862
Total TN	2714788
Total FP	1364
Total FP CONTRA	149
Total FP INCONS	1089
Total FP COMP	126
Total FN	2017

Total Scores
MCC	0.536
Average MCC ± 95% Confidence Intervals	0.661 ± 0.062
Sensitivity	0.480
Positive Predictive Value	0.601
Nr of predictions	93

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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
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
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_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
2YIE_X	-	0.34	0.33	0.36	4	1367	7	2	5	0	8
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_g	-	-0.01	0.00	0.00	0	458	7	2	5	0	4
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_1	-	0.76	0.63	0.92	12	1212	3	0	1	2	7
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_2	-	0.27	0.27	0.28	9	6184	26	2	21	3	24
3J16_L	tRNA links to Rfam database...	0.35	0.33	0.38	10	2749	16	1	15	0	20
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.50	0.43	0.57	272	1116290	208	11	192	5	361
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
3J2C_M	-	0.37	0.30	0.45	63	106352	79	9	67	3	144
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_F	-	0.00	0.00	0.00	0	2620	11	2	6	3	12
3ZEX_G	-	0.77	0.66	0.91	49	16417	10	0	5	5	25
3ZEX_E	-	0.00	0.00	0.00	0	21886	61	2	57	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.77	0.67	0.89	33	6984	4	0	4	0	16
3ZEX_B	-	0.29	0.26	0.33	146	1071940	307	34	260	13	412
3ZEX_H	-	0.19	0.18	0.19	7	9009	29	4	25	0	31
3ZEX_C	5_8S_rRNA links to Rfam database...	0.38	0.31	0.47	16	14162	21	2	16	3	36
4A1C_3	5S_rRNA links to Rfam database...	0.73	0.61	0.87	33	7102	6	1	4	1	21
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.12	5	11738	49	7	31	11	28
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
4FNJ_A	-	0.66	0.50	0.89	8	586	1	0	1	0	8
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
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	0	0	0

^top

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 Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

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

Performance of ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

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