CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Fold		Vsfold4
MCC	0.656	>	0.550
Average MCC ± 95% Confidence Intervals	0.709 ± 0.061	>	0.643 ± 0.062
Sensitivity	0.594	>	0.470
Positive Predictive Value	0.730	>	0.648
Total TP	1488	>	1179
Total TN	401487	<	401705
Total FP	644	<	704
Total FP CONTRA	71	>	65
Total FP INCONS	479	<	576
Total FP COMP	94	>	63
Total FN	1019	<	1328
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP	1488
Total TN	401487
Total FP	644
Total FP CONTRA	71
Total FP INCONS	479
Total FP COMP	94
Total FN	1019

Total Scores
MCC	0.656
Average MCC ± 95% Confidence Intervals	0.709 ± 0.061
Sensitivity	0.594
Positive Predictive Value	0.730
Nr of predictions	93

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KPV_A	-	0.96	0.92	1.00	12	549	0	0	0	0	1
2KRL_A	-	0.76	0.60	0.96	24	5126	5	0	1	4	16
2KU0_A	-	0.83	0.69	1.00	11	692	0	0	0	0	5
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
2KXM_A	-	0.83	0.70	1.00	7	344	0	0	0	0	3
2KZL_A	-	0.86	0.74	1.00	14	1471	0	0	0	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.90	0.88	0.92	22	2121	2	0	2	0	3
2L1F_A	Gammaretro_CES links to Rfam database...	0.89	0.88	0.91	21	2057	2	0	2	0	3
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	-	0.39	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...	-0.01	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	0.79	0.91	31	6071	5	0	3	2	8
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.96	0.92	1.00	12	484	0	0	0	0	1
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2WWQ_V	tRNA links to Rfam database...	0.76	0.64	0.90	18	2906	3	0	2	1	10
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...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.93	0.86	1.00	36	5115	0	0	0	0	6
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	-	0.25	0.25	0.27	3	1367	8	2	6	0	9
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
3ADB_C	-	0.80	0.74	0.88	28	4154	4	0	4	0	10
3AKZ_H	tRNA links to Rfam database...	0.84	0.75	0.95	21	2679	1	1	0	0	7
3AM1_B	-	0.78	0.71	0.86	25	3211	4	0	4	0	10
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3IYQ_A	tmRNA links to Rfam database...	0.29	0.31	0.27	29	60618	83	20	59	4	65
3IZ4_A	tmRNA links to Rfam database...	0.53	0.46	0.61	61	70776	44	5	34	5	71
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	6864	7	1	6	0	22
3J0L_a	-	0.20	0.19	0.23	3	1115	10	2	8	0	13
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_2	-	0.25	0.24	0.26	8	6185	25	2	21	2	25
3J0L_1	-	0.76	0.63	0.92	12	1212	2	0	1	1	7
3J0L_h	-	0.81	0.65	1.00	28	6077	2	0	0	2	15
3J0L_7	-	-0.01	0.00	0.00	0	1213	12	0	12	0	17
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J16_L	tRNA links to Rfam database...	0.63	0.53	0.76	16	2754	5	0	5	0	14
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.45	0.40	0.52	12	2827	12	0	11	1	18
3J2C_O	-	0.59	0.54	0.65	34	10244	18	1	17	0	29
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
3NDB_M	-	0.84	0.74	0.96	45	9133	3	0	2	1	16
3NKB_B	-	0.35	0.31	0.42	8	1997	11	0	11	0	18
3NMU_E	-	-0.01	0.00	0.00	0	552	11	2	7	2	6
3NPB_A	SAM links to Rfam database...	0.70	0.61	0.80	28	6986	10	1	6	3	18
3O58_2	5S_rRNA links to Rfam database...	0.71	0.71	0.71	27	7222	12	3	8	1	11
3O58_3	5_8S_rRNA links to Rfam database...	0.29	0.31	0.28	11	12363	41	3	26	12	24
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...	0.77	0.64	0.94	46	12831	5	0	3	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...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.57	0.48	0.69	20	3887	9	1	8	0	22
3SIU_F	-	0.85	0.73	1.00	8	370	0	0	0	0	3
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	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	-	0.45	0.35	0.59	13	3138	9	1	8	0	24
3UZL_B	tRNA links to Rfam database...	0.77	0.62	0.96	23	3546	1	0	1	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...	0.85	0.75	0.97	30	4722	2	0	1	1	10
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.67	0.87	33	6983	5	1	4	0	16
3ZEX_G	-	0.76	0.65	0.89	48	16417	12	0	6	6	26
3ZEX_E	-	0.00	0.00	0.00	0	21890	57	2	53	2	77
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11744	43	5	27	11	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.57	0.82	31	7102	7	1	6	0	23
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...	0.32	0.26	0.42	5	1263	7	1	6	0	14
4ENC_A	crcB links to Rfam database...	0.31	0.26	0.38	5	1313	8	1	7	0	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.24	0.22	0.27	7	3460	19	3	16	0	25
4HXH_A	-	1.00	1.00	1.00	6	319	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	1179
Total TN	401705
Total FP	704
Total FP CONTRA	65
Total FP INCONS	576
Total FP COMP	63
Total FN	1328

Total Scores
MCC	0.550
Average MCC ± 95% Confidence Intervals	0.643 ± 0.062
Sensitivity	0.470
Positive Predictive Value	0.648
Nr of predictions	93

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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
2KPV_A	-	0.96	0.92	1.00	12	549	0	0	0	0	1
2KRL_A	-	0.65	0.53	0.81	21	5125	7	0	5	2	19
2KU0_A	-	-0.02	0.00	0.00	0	694	9	0	9	0	16
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
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...	0.68	0.56	0.82	14	2128	3	0	3	0	11
2L1F_A	Gammaretro_CES links to Rfam database...	0.66	0.54	0.81	13	2064	3	0	3	0	11
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...	0.92	0.85	1.00	17	973	0	0	0	0	3
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	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...	-0.01	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	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.31	0.28	0.34	11	6073	21	3	18	0	28
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
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
2WWQ_V	tRNA links to Rfam database...	0.64	0.50	0.82	14	2909	4	0	3	1	14
2XKV_B	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	4533	27	8	19	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	5122	29	1	28	0	42
2Y8W_B	-	1.00	1.00	1.00	6	184	1	0	0	1	0
2Y9C_V	-	0.63	0.50	0.80	12	2263	4	0	3	1	12
2YIE_X	-	0.36	0.33	0.40	4	1368	6	2	4	0	8
2YIE_Z	-	-0.01	0.00	0.00	0	1529	11	3	8	0	12
3ADB_C	-	0.89	0.79	1.00	30	4156	0	0	0	0	8
3AKZ_H	tRNA links to Rfam database...	0.67	0.57	0.80	16	2681	5	1	3	1	12
3AM1_B	-	0.84	0.71	1.00	25	3215	0	0	0	0	10
3AMU_B	tRNA links to Rfam database...	0.64	0.56	0.75	15	2983	7	0	5	2	12
3IYQ_A	tmRNA links to Rfam database...	0.29	0.29	0.29	27	60634	71	13	52	6	67
3IZ4_A	tmRNA links to Rfam database...	0.36	0.31	0.43	41	70780	59	7	48	4	91
3IZF_C	5S_rRNA links to Rfam database...	0.69	0.56	0.86	30	6868	5	0	5	0	24
3J0L_a	-	0.39	0.31	0.50	5	1118	5	2	3	0	11
3J0L_8	-	0.70	0.50	1.00	4	186	0	0	0	0	4
3J0L_2	-	0.38	0.36	0.41	12	6187	18	3	14	1	21
3J0L_1	-	0.28	0.21	0.40	4	1215	6	1	5	0	15
3J0L_h	-	0.38	0.28	0.52	12	6082	11	0	11	0	31
3J0L_7	-	0.51	0.41	0.64	7	1214	4	0	4	0	10
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
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...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J2C_O	-	0.30	0.24	0.39	15	10258	24	0	23	1	48
3J2L_3	5S_rRNA links to Rfam database...	0.57	0.45	0.73	24	7842	12	1	8	3	29
3NDB_M	-	0.28	0.23	0.35	14	9140	26	0	26	0	47
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NMU_E	-	0.41	0.17	1.00	1	560	3	0	0	3	5
3NPB_A	SAM links to Rfam database...	0.61	0.50	0.74	23	6990	9	0	8	1	23
3O58_2	5S_rRNA links to Rfam database...	0.47	0.42	0.53	16	7230	16	3	11	2	22
3O58_3	5_8S_rRNA links to Rfam database...	0.09	0.09	0.10	3	12373	35	5	22	8	32
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...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.19	0.17	0.24	7	3887	22	1	21	0	35
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...	0.53	0.41	0.71	15	3549	6	1	5	0	22
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.67	0.58	0.79	23	4724	7	0	6	1	17
3ZEX_D	5S_rRNA links to Rfam database...	0.55	0.45	0.69	22	6989	10	0	10	0	27
3ZEX_G	-	0.30	0.23	0.39	17	16427	27	2	25	0	57
3ZEX_E	-	0.08	0.06	0.11	5	21900	40	1	39	0	72
4A1C_2	5_8S_rRNA links to Rfam database...	0.28	0.24	0.33	8	11757	28	0	16	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...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ATO_G	-	0.32	0.30	0.38	3	520	5	1	4	0	7
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...	0.69	0.47	1.00	9	1317	0	0	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.56	0.47	0.68	15	3464	7	1	6	0	17
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 Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

2. Individual counts for Fold [ 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 ]