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		Vsfold4
MCC	0.727	>	0.607
Average MCC ± 95% Confidence Intervals	0.770 ± 0.066	>	0.698 ± 0.067
Sensitivity	0.758	>	0.600
Positive Predictive Value	0.703	>	0.622
Total TP	1272	>	1007
Total TN	145931	<	146121
Total FP	762	>	731
Total FP CONTRA	192	>	172
Total FP INCONS	346	<	441
Total FP COMP	224	>	118
Total FN	405	<	670
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of ProbKnot and Vsfold4. 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 Vsfold4).
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 Vsfold4).
Comparison of average Matthews Correlation Coefficients (MCCs) for ProbKnot and Vsfold4. 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 Vsfold4).

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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	1272
Total TN	145931
Total FP	762
Total FP CONTRA	192
Total FP INCONS	346
Total FP COMP	224
Total FN	405

Total Scores
MCC	0.727
Average MCC ± 95% Confidence Intervals	0.770 ± 0.066
Sensitivity	0.758
Positive Predictive Value	0.703
Nr of predictions	85

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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	-	0.82	0.87	0.77	20	1998	15	6	0	9	3
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2KXM_A	-	0.87	0.88	0.88	7	141	1	0	1	0	1
2KZL_A	-	1.00	1.00	1.00	13	507	2	0	0	2	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	0	0	0	0	0
2L1F_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L2K_A	-	1.00	1.00	1.00	17	332	0	0	0	0	0
2L3C_B	-	1.00	1.00	1.00	14	225	0	0	0	0	0
2L3E_A	-	1.00	1.00	1.00	12	228	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	1.00	1.00	1.00	30	955	0	0	0	0	0
2L5Z_A	-	1.00	1.00	1.00	9	102	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LA5_A	-	0.85	0.86	0.86	6	268	3	0	1	2	1
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.89	0.86	0.93	25	2413	9	0	2	7	4
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	1.00	1.00	1.00	11	196	1	0	0	1	0
2RRC_A	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	26	0	6	20	3
2XQD_Y	tRNA links to Rfam database...	1.00	1.00	1.00	21	1108	2	0	0	2	0
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.25	0.26	0.26	9	2011	26	1	24	1	26
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
2Y9C_V	-	0.79	0.83	0.75	15	886	8	0	5	3	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2YIE_X	-	0.53	0.57	0.50	4	536	7	1	3	3	3
3AKZ_H	tRNA links to Rfam database...	0.87	1.00	0.77	20	1101	9	6	0	3	0
3AM1_B	-	0.82	0.86	0.78	25	1434	7	3	4	0	4
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	9	0	5	4	4
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.18	17	22346	97	41	36	20	34
3IZ4_A	tmRNA links to Rfam database...	0.59	0.61	0.57	58	25435	49	17	26	6	37
3IZF_C	5S_rRNA links to Rfam database...	0.90	0.91	0.89	32	2604	7	0	4	3	3
3J0L_1	-	0.83	0.77	0.91	10	473	5	0	1	4	3
3J0L_g	-	-0.02	0.00	0.00	0	171	7	1	4	2	2
3J0L_2	-	0.30	0.31	0.31	8	2224	27	1	17	9	18
3J0L_7	-	-0.02	0.00	0.00	0	506	13	3	10	0	10
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.60	0.64	0.58	7	399	6	4	1	1	4
3J0L_h	-	0.89	0.88	0.90	28	2109	3	0	3	0	4
3J16_L	tRNA links to Rfam database...	0.42	0.48	0.38	10	1133	16	3	13	0	11
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	8	0	5	3	5
3J2C_O	-	0.72	0.73	0.71	30	3945	18	5	7	6	11
3J2L_3	5S_rRNA links to Rfam database...	0.79	0.76	0.81	26	2988	11	0	6	5	8
3NDB_M	-	0.94	0.93	0.95	41	3671	8	0	2	6	3
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NMU_E	-	-0.02	0.00	0.00	0	207	11	6	3	2	3
3NPB_A	SAM links to Rfam database...	0.79	0.73	0.87	27	2247	9	0	4	5	10
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.50	0.29	11	4726	42	10	17	15	11
3O58_2	5S_rRNA links to Rfam database...	0.91	0.94	0.88	29	2721	10	0	4	6	2
3OVB_D	-	1.00	1.00	1.00	11	215	2	0	0	2	0
3OVS_D	-	1.00	1.00	1.00	12	204	1	0	0	1	0
3P22_G	-	1.00	1.00	1.00	11	301	1	0	0	1	0
3PDR_A	ykoK links to Rfam database...	0.88	0.92	0.85	46	4786	10	5	3	2	4
3R4F_A	-	1.00	1.00	1.00	22	884	1	0	0	1	0
3R9X_C	-	1.00	1.00	1.00	8	221	2	0	0	2	0
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.66	0.69	0.65	20	1502	11	6	5	0	9
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
3SN2_B	IRE_II links to Rfam database...	1.00	1.00	1.00	12	142	0	0	0	0	0
3TRZ_Z	-	1.00	1.00	1.00	5	87	2	0	0	2	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
3UZL_B	tRNA links to Rfam database...	0.92	1.00	0.84	16	1274	11	3	0	8	0
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.98	0.97	1.00	32	1957	1	0	0	1	1
3ZEX_G	-	0.98	0.96	1.00	43	6464	16	0	0	16	2
3ZEX_D	5S_rRNA links to Rfam database...	0.90	0.86	0.94	30	2764	7	0	2	5	5
3ZEX_E	-	-0.01	0.00	0.00	0	8245	61	25	34	2	34
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.25	0.13	5	4477	49	13	21	15	15
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	7	0	4	3	5
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	1	1	0	0	4
4ENC_A	crcB links to Rfam database...	0.52	0.53	0.53	8	481	8	0	7	1	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.38	0.38	0.41	9	1180	13	6	7	0	15
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

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Performance of Vsfold4 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold4

Total Base Pair Counts
Total TP	1007
Total TN	146121
Total FP	731
Total FP CONTRA	172
Total FP INCONS	441
Total FP COMP	118
Total FN	670

Total Scores
MCC	0.607
Average MCC ± 95% Confidence Intervals	0.698 ± 0.067
Sensitivity	0.600
Positive Predictive Value	0.622
Nr of predictions	85

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2. Individual counts for Vsfold4 [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.84	0.83	0.86	19	2002	9	2	1	6	4
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2KXM_A	-	0.78	0.63	1.00	5	144	0	0	0	0	3
2KZL_A	-	1.00	1.00	1.00	13	507	1	0	0	1	0
2L1F_B	Gammaretro_CES links to Rfam database...	0.69	0.58	0.82	14	774	3	0	3	0	10
2L1F_A	Gammaretro_CES links to Rfam database...	0.67	0.57	0.81	13	747	3	0	3	0	10
2L2K_A	-	0.94	0.88	1.00	15	334	0	0	0	0	2
2L3C_B	-	1.00	1.00	1.00	14	225	0	0	0	0	0
2L3E_A	-	1.00	1.00	1.00	12	228	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	0.93	0.87	1.00	26	959	0	0	0	0	4
2L5Z_A	-	0.68	0.67	0.75	6	103	2	0	2	0	3
2L94_A	HIV_FE links to Rfam database...	0.94	0.89	1.00	16	341	1	0	0	1	2
2LA5_A	-	0.77	0.71	0.83	5	269	1	0	1	0	2
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	515	13	0	13	0	18
2LDL_A	-	0.94	0.89	1.00	8	132	1	0	0	1	1
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.35	0.38	0.34	11	2408	21	7	14	0	18
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
2RRC_A	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2XKV_B	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	1808	27	13	14	0	11
2XQD_Y	tRNA links to Rfam database...	0.95	0.90	1.00	19	1110	1	0	0	1	2
2XXA_G	Bacteria_small_SRP links to Rfam database...	-0.02	0.00	0.00	0	2016	29	1	28	0	35
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
2Y9C_V	-	0.75	0.67	0.86	12	892	4	0	2	2	6
2YIE_Z	-	-0.02	0.00	0.00	0	591	11	5	6	0	8
2YIE_X	-	0.53	0.57	0.50	4	536	6	1	3	2	3
3AKZ_H	tRNA links to Rfam database...	0.77	0.75	0.79	15	1108	6	2	2	2	5
3AM1_B	-	0.93	0.86	1.00	25	1441	0	0	0	0	4
3AMU_B	tRNA links to Rfam database...	0.73	0.74	0.74	14	1138	8	0	5	3	5
3IYQ_A	tmRNA links to Rfam database...	0.27	0.35	0.21	18	22353	80	40	29	11	33
3IZ4_A	tmRNA links to Rfam database...	0.39	0.39	0.39	37	25441	63	15	43	5	58
3IZF_C	5S_rRNA links to Rfam database...	0.85	0.83	0.88	29	2607	6	0	4	2	6
3J0L_1	-	0.26	0.23	0.33	3	475	7	2	4	1	10
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_2	-	0.47	0.46	0.50	12	2226	18	1	11	6	14
3J0L_7	-	0.69	0.70	0.70	7	509	4	1	2	1	3
3J0L_8	-	0.74	0.57	1.00	4	72	0	0	0	0	3
3J0L_a	-	0.39	0.36	0.44	4	402	6	4	1	1	7
3J0L_h	-	0.44	0.38	0.52	12	2117	11	2	9	0	20
3J16_L	tRNA links to Rfam database...	0.98	0.95	1.00	20	1139	0	0	0	0	1
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	7	0	5	2	5
3J2C_O	-	0.33	0.32	0.36	13	3951	26	3	20	3	28
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.71	0.73	24	2987	12	3	6	3	10
3NDB_M	-	0.33	0.32	0.35	14	3674	26	2	24	0	30
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NMU_E	-	0.57	0.33	1.00	1	215	3	0	0	3	2
3NPB_A	SAM links to Rfam database...	0.66	0.59	0.73	22	2248	10	0	8	2	15
3O58_3	5_8S_rRNA links to Rfam database...	0.12	0.14	0.11	3	4737	35	8	16	11	19
3O58_2	5S_rRNA links to Rfam database...	0.53	0.52	0.55	16	2725	16	3	10	3	15
3OVB_D	-	1.00	1.00	1.00	11	215	1	0	0	1	0
3OVS_D	-	1.00	1.00	1.00	12	204	0	0	0	0	0
3P22_G	-	1.00	1.00	1.00	11	301	0	0	0	0	0
3PDR_A	ykoK links to Rfam database...	0.69	0.64	0.74	32	4797	13	3	8	2	18
3R4F_A	-	0.98	0.95	1.00	21	885	1	0	0	1	1
3R9X_C	-	1.00	1.00	1.00	8	221	2	0	0	2	0
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.23	0.24	0.24	7	1504	22	5	17	0	22
3SIU_F	-	0.86	0.75	1.00	6	139	0	0	0	0	2
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3TRZ_Z	-	1.00	1.00	1.00	5	87	1	0	0	1	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3UZL_B	tRNA links to Rfam database...	0.66	0.69	0.65	11	1276	10	3	3	4	5
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.74	0.70	0.79	23	1960	7	1	5	1	10
3ZEX_G	-	0.31	0.29	0.34	13	6469	31	5	20	6	32
3ZEX_D	5S_rRNA links to Rfam database...	0.66	0.63	0.71	22	2765	10	4	5	1	13
3ZEX_E	-	0.12	0.15	0.11	5	8259	40	13	27	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.36	0.40	0.33	8	4492	28	4	12	12	12
4A1C_3	5S_rRNA links to Rfam database...	0.29	0.30	0.31	11	2727	26	4	21	1	26
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.77	0.60	1.00	9	487	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

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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 Vsfold4 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold4

2. Individual counts for Vsfold4 [ download as .csv ]