CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ContextFold		RNAwolf
MCC	0.566	>	0.343
Average MCC ± 95% Confidence Intervals	0.644 ± 0.081	>	0.470 ± 0.089
Sensitivity	0.469	>	0.318
Positive Predictive Value	0.684	>	0.371
Total TP	1417	>	962
Total TN	2526599	>	2526076
Total FP	729	<	1721
Total FP CONTRA	68	<	187
Total FP INCONS	586	<	1445
Total FP COMP	75	<	89
Total FN	1604	<	2059
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of ContextFold and RNAwolf. 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 ContextFold and RNAwolf).
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 ContextFold and RNAwolf).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and RNAwolf. 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 ContextFold and RNAwolf).

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Performance of ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP	1417
Total TN	2526599
Total FP	729
Total FP CONTRA	68
Total FP INCONS	586
Total FP COMP	75
Total FN	1604

Total Scores
MCC	0.566
Average MCC ± 95% Confidence Intervals	0.644 ± 0.081
Sensitivity	0.469
Positive Predictive Value	0.684
Nr of predictions	61

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.55	0.50	0.63	10	1524	6	0	6	0	10
2LDL_A	-	0.90	0.82	1.00	9	342	0	0	0	0	2
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	-	0.93	0.88	1.00	7	344	2	0	0	2	1
2LK3_A	-	0.89	0.80	1.00	8	268	0	0	0	0	2
2LKR_A	-	0.65	0.56	0.76	22	6076	9	0	7	2	17
2LQZ_A	-	0.80	0.73	0.89	8	342	1	1	0	0	3
2LU0_A	-	1.00	1.00	1.00	16	1160	0	0	0	0	0
2LWK_A	-	0.88	0.85	0.92	11	484	1	0	1	0	2
2M58_A	-	-0.01	0.00	0.00	0	1639	14	0	14	0	17
3J0L_2	-	0.64	0.61	0.69	20	6187	11	2	7	2	13
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.71	0.56	0.90	9	1118	1	0	1	0	7
3J0L_1	-	0.70	0.58	0.85	11	1212	3	0	2	1	8
3J0L_h	-	0.82	0.67	1.00	29	6076	2	0	0	2	14
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_g	-	-0.01	0.00	0.00	0	462	3	1	2	0	4
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.73	0.61	0.87	387	1116318	63	8	52	3	246
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...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J2C_M	-	0.72	0.57	0.92	118	106363	13	2	8	3	89
3J2C_O	-	0.83	0.70	1.00	44	10252	1	0	0	1	19
3J2L_3	5S_rRNA links to Rfam database...	0.79	0.62	1.00	33	7842	2	0	0	2	20
3J3D_C	tRNA links to Rfam database...	0.73	0.61	0.89	17	2756	2	0	2	0	11
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7483	29	9	11	9	33
3J3E_7	5S_rRNA links to Rfam database...	0.72	0.56	0.94	30	7108	2	0	2	0	24
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.31	0.37	11	12216	29	3	16	10	25
3J3F_7	5S_rRNA links to Rfam database...	0.81	0.68	0.97	34	7225	1	0	1	0	16
3J3V_B	5S_rRNA links to Rfam database...	0.76	0.58	1.00	33	6988	0	0	0	0	24
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	0	0	0	0	1
3TS0_U	-	1.00	1.00	1.00	6	247	0	0	0	0	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.75	0.57	1.00	21	3139	0	0	0	0	16
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W1K_J	tRNA-Sec links to Rfam database...	0.81	0.71	0.93	27	4157	2	1	1	0	11
3W3S_B	tRNA-Sec links to Rfam database...	0.79	0.70	0.90	28	4722	4	0	3	1	12
3ZEX_H	-	0.22	0.21	0.24	8	9011	26	2	24	0	30
3ZEX_F	-	0.00	0.00	0.00	0	2617	16	2	9	5	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.33	0.25	0.45	13	14167	22	1	15	6	39
3ZEX_B	-	0.19	0.15	0.23	86	1072008	291	21	265	5	472
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.67	0.97	33	6987	1	0	1	0	16
3ZEX_E	-	0.08	0.06	0.10	5	21896	44	5	39	0	72
3ZEX_G	-	0.26	0.20	0.33	15	16426	34	2	28	4	59
3ZND_W	tRNA links to Rfam database...	0.21	0.22	0.22	5	2980	20	0	18	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28
4A1C_3	5S_rRNA links to Rfam database...	0.78	0.63	0.97	34	7105	1	0	1	0	20
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.52	0.40	0.68	17	4346	9	1	7	1	25
4ATO_G	-	-0.01	0.00	0.00	0	526	2	0	2	0	10
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FNJ_A	-	0.79	0.63	1.00	10	585	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.71	0.56	0.90	18	3466	2	1	1	0	14
4FRN_A	AdoCbl-variant links to Rfam database...	0.40	0.33	0.50	12	5127	12	3	9	0	24
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	0	0	0
4JF2_A	preQ1-II links to Rfam database...	0.50	0.39	0.67	12	2832	6	2	4	0	19
4JRC_A	-	0.78	0.61	1.00	14	1526	0	0	0	0	9

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Performance of RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

Total Base Pair Counts
Total TP	962
Total TN	2526076
Total FP	1721
Total FP CONTRA	187
Total FP INCONS	1445
Total FP COMP	89
Total FN	2059

Total Scores
MCC	0.343
Average MCC ± 95% Confidence Intervals	0.470 ± 0.089
Sensitivity	0.318
Positive Predictive Value	0.371
Nr of predictions	61

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.52	0.50	0.56	10	1522	8	0	8	0	10
2LDL_A	-	0.74	0.64	0.88	7	343	1	0	1	0	4
2LHP_A	-	1.00	1.00	1.00	16	650	1	0	0	1	0
2LI4_A	-	0.97	0.94	1.00	15	481	0	0	0	0	1
2LJJ_A	-	1.00	1.00	1.00	8	343	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	10	266	0	0	0	0	0
2LKR_A	-	0.81	0.74	0.88	29	6072	8	0	4	4	10
2LQZ_A	-	0.91	0.91	0.91	10	340	1	1	0	0	1
2LU0_A	-	0.97	0.94	1.00	15	1161	3	0	0	3	1
2LWK_A	-	0.37	0.38	0.38	5	483	9	0	8	1	8
2M58_A	-	0.51	0.47	0.57	8	1639	6	3	3	0	9
3J0L_2	-	0.11	0.12	0.11	4	6181	34	5	26	3	29
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.18	0.19	0.20	3	1113	12	1	11	0	13
3J0L_1	-	0.68	0.63	0.75	12	1209	5	0	4	1	7
3J0L_h	-	0.33	0.30	0.37	13	6070	24	0	22	2	30
3J0L_7	-	-0.01	0.00	0.00	0	1214	11	0	11	0	17
3J0L_g	-	0.16	0.25	0.11	1	456	8	6	2	0	3
3J16_L	tRNA links to Rfam database...	0.45	0.40	0.52	12	2752	11	0	11	0	18
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.45	0.42	0.49	266	1116224	283	17	258	8	367
3J20_1	tRNA links to Rfam database...	0.46	0.52	0.41	12	2897	17	6	11	0	11
3J20_0	tRNA links to Rfam database...	0.40	0.40	0.41	12	2821	18	0	17	1	18
3J2C_M	-	0.19	0.17	0.21	35	106323	133	11	122	0	172
3J2C_O	-	0.40	0.37	0.44	23	10244	30	0	29	1	40
3J2L_3	5S_rRNA links to Rfam database...	0.55	0.49	0.62	26	7833	18	0	16	2	27
3J3D_C	tRNA links to Rfam database...	0.79	0.75	0.84	21	2750	5	2	2	1	7
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7470	42	4	29	9	33
3J3E_7	5S_rRNA links to Rfam database...	0.41	0.35	0.49	19	7101	20	1	19	0	35
3J3F_8	5_8S_rRNA links to Rfam database...	0.23	0.25	0.21	9	12204	45	5	28	12	27
3J3F_7	5S_rRNA links to Rfam database...	0.21	0.20	0.23	10	7216	34	2	32	0	40
3J3V_B	5S_rRNA links to Rfam database...	0.43	0.37	0.51	21	6980	20	2	18	0	36
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	0	0	0	0	1
3TS0_U	-	1.00	1.00	1.00	6	247	2	0	0	2	0
3TS2_V	-	-0.02	0.00	0.00	0	270	7	0	6	1	5
3U4M_B	-	0.44	0.38	0.52	14	3133	13	0	13	0	23
3UZL_B	tRNA links to Rfam database...	0.72	0.59	0.88	22	3545	4	1	2	1	15
3VJR_D	-	1.00	1.00	1.00	13	617	1	0	0	1	0
3W1K_J	tRNA-Sec links to Rfam database...	0.71	0.66	0.78	25	4154	7	0	7	0	13
3W3S_B	tRNA-Sec links to Rfam database...	0.68	0.63	0.74	25	4719	10	0	9	1	15
3ZEX_H	-	0.00	0.00	0.00	0	9006	40	8	31	1	38
3ZEX_F	-	-0.01	0.00	0.00	0	2613	20	6	9	5	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.05	0.06	0.06	3	14144	49	12	37	0	49
3ZEX_B	-	0.14	0.13	0.15	70	1071902	417	55	353	9	488
3ZEX_D	5S_rRNA links to Rfam database...	0.20	0.18	0.22	9	6980	32	3	29	0	40
3ZEX_E	-	0.00	0.00	0.00	0	21876	69	10	59	0	77
3ZEX_G	-	0.20	0.18	0.23	13	16415	43	6	37	0	61
3ZND_W	tRNA links to Rfam database...	0.50	0.48	0.52	11	2982	13	0	10	3	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.09	0.08	3	11741	46	10	27	9	30
4A1C_3	5S_rRNA links to Rfam database...	0.23	0.20	0.28	11	7101	28	2	26	0	43
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.23	0.19	0.30	8	4344	20	1	18	1	34
4ATO_G	-	-0.02	0.00	0.00	0	520	8	1	7	0	10
4ENB_A	crcB links to Rfam database...	0.35	0.32	0.40	6	1260	9	1	8	0	13
4ENC_A	crcB links to Rfam database...	0.34	0.32	0.38	6	1310	10	1	9	0	13
4FNJ_A	-	-0.02	0.00	0.00	0	587	8	0	8	0	16
4FRG_B	AdoCbl-variant links to Rfam database...	0.56	0.50	0.64	16	3461	10	1	8	1	16
4FRN_A	AdoCbl-variant links to Rfam database...	-0.01	0.00	0.00	0	5119	32	0	32	0	36
4HXH_A	-	1.00	1.00	1.00	6	319	2	0	0	2	0
4JF2_A	preQ1-II links to Rfam database...	0.67	0.58	0.78	18	2827	5	3	2	0	13
4JRC_A	-	0.58	0.52	0.67	12	1522	6	0	6	0	11

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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 ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

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

Performance of RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

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