CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Sfold		RNAwolf
MCC	0.506	>	0.356
Average MCC ± 95% Confidence Intervals	0.607 ± 0.073	>	0.486 ± 0.083
Sensitivity	0.428	>	0.331
Positive Predictive Value	0.598	>	0.386
Total TP	1366	>	1055
Total TN	2539773	>	2539321
Total FP	1013	<	1777
Total FP CONTRA	87	<	192
Total FP INCONS	831	<	1489
Total FP COMP	95	<	96
Total FN	1822	<	2133
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP	1366
Total TN	2539773
Total FP	1013
Total FP CONTRA	87
Total FP INCONS	831
Total FP COMP	95
Total FN	1822

Total Scores
MCC	0.506
Average MCC ± 95% Confidence Intervals	0.607 ± 0.073
Sensitivity	0.428
Positive Predictive Value	0.598
Nr of predictions	69

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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	0	5	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	-	0.89	0.79	1.00	31	6074	1	0	0	1	8
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
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	-	0.29	0.18	0.50	3	1647	3	1	2	0	14
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
2YIE_X	-	0.58	0.33	1.00	4	1374	0	0	0	0	8
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3J0L_g	-	-0.01	0.00	0.00	0	460	5	1	4	0	4
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_a	-	0.51	0.50	0.53	8	1113	7	3	4	0	8
3J0L_1	-	0.76	0.63	0.92	12	1212	3	0	1	2	7
3J0L_h	-	0.75	0.60	0.93	26	6077	4	0	2	2	17
3J0L_7	-	-0.01	0.00	0.00	0	1222	3	0	3	0	17
3J0L_2	-	0.36	0.33	0.39	11	6188	19	2	15	2	22
3J16_L	tRNA links to Rfam database...	0.29	0.23	0.37	7	2756	12	0	12	0	23
3J20_1	tRNA links to Rfam database...	0.73	0.70	0.76	16	2905	6	0	5	1	7
3J20_0	tRNA links to Rfam database...	0.43	0.40	0.48	12	2825	14	0	13	1	18
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.47	0.41	0.55	261	1116287	220	14	203	3	372
3J2C_O	-	0.64	0.48	0.86	30	10261	6	0	5	1	33
3J2C_M	-	0.63	0.49	0.80	102	106363	31	3	23	5	105
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
3J3D_C	tRNA links to Rfam database...	0.36	0.25	0.54	7	2762	6	0	6	0	21
3J3E_7	5S_rRNA links to Rfam database...	0.60	0.50	0.73	27	7103	10	1	9	0	27
3J3E_8	5_8S_rRNA links to Rfam database...	0.06	0.06	0.08	2	7477	32	2	22	8	31
3J3F_8	5_8S_rRNA links to Rfam database...	0.35	0.33	0.38	12	12214	34	3	17	14	24
3J3F_7	5S_rRNA links to Rfam database...	0.69	0.60	0.79	30	7222	8	1	7	0	20
3J3V_B	5S_rRNA links to Rfam database...	0.51	0.37	0.72	21	6992	8	0	8	0	36
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...	0.65	0.50	0.84	21	3891	4	1	3	0	21
3SIU_F	-	0.85	0.73	1.00	8	370	0	0	0	0	3
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	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	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.51	0.32	0.80	12	3555	3	2	1	0	25
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
3W3S_B	tRNA-Sec links to Rfam database...	0.57	0.53	0.64	21	4720	13	1	11	1	19
3ZEX_H	-	0.19	0.18	0.19	7	9009	29	5	24	0	31
3ZEX_F	-	0.00	0.00	0.00	0	2623	7	2	3	2	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.21	0.48	11	14173	26	1	11	14	41
3ZEX_G	-	0.78	0.68	0.91	50	16416	9	0	5	4	24
3ZEX_E	-	0.00	0.00	0.00	0	21891	56	3	51	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.74	0.63	0.86	31	6985	5	0	5	0	18
3ZEX_B	-	0.31	0.27	0.36	152	1071959	280	27	242	11	406
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	22	1	20	1	18
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11751	34	2	23	9	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	-	0.31	0.10	1.00	1	527	0	0	0	0	9
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...	0.51	0.26	1.00	5	1321	0	0	0	0	14
4FNJ_A	-	0.79	0.63	1.00	10	585	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.62	0.47	0.83	15	3468	3	1	2	0	17
4FRN_A	AdoCbl-variant links to Rfam database...	0.63	0.44	0.89	16	5133	2	2	0	0	20
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	0	0	0
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12
4JRC_A	-	0.29	0.26	0.35	6	1523	11	0	11	0	17

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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	1055
Total TN	2539321
Total FP	1777
Total FP CONTRA	192
Total FP INCONS	1489
Total FP COMP	96
Total FN	2133

Total Scores
MCC	0.356
Average MCC ± 95% Confidence Intervals	0.486 ± 0.083
Sensitivity	0.331
Positive Predictive Value	0.386
Nr of predictions	69

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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
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
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
2LDT_A	-	0.86	0.80	0.92	12	452	1	0	1	0	3
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
2YIE_Z	-	0.43	0.42	0.45	5	1529	9	1	5	3	7
2YIE_X	-	-0.01	0.00	0.00	0	1364	15	4	10	1	12
3AMU_B	tRNA links to Rfam database...	0.68	0.63	0.74	17	2980	9	0	6	3	10
3J0L_g	-	0.16	0.25	0.11	1	456	8	6	2	0	3
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_2	-	0.11	0.12	0.11	4	6181	34	5	26	3	29
3J16_L	tRNA links to Rfam database...	0.45	0.40	0.52	12	2752	11	0	11	0	18
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
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.45	0.42	0.49	266	1116224	283	17	258	8	367
3J2C_O	-	0.40	0.37	0.44	23	10244	30	0	29	1	40
3J2C_M	-	0.19	0.17	0.21	35	106323	133	11	122	0	172
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_7	5S_rRNA links to Rfam database...	0.41	0.35	0.49	19	7101	20	1	19	0	35
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7470	42	4	29	9	33
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
3RKF_A	Purine links to Rfam database...	0.72	0.62	0.84	21	2186	4	0	4	0	13
3SD1_A	THF links to Rfam database...	0.46	0.43	0.50	18	3880	18	0	18	0	24
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	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_G	-	0.20	0.18	0.23	13	16415	43	6	37	0	61
3ZEX_E	-	0.00	0.00	0.00	0	21876	69	10	59	0	77
3ZEX_D	5S_rRNA links to Rfam database...	0.20	0.18	0.22	9	6980	32	3	29	0	40
3ZEX_B	-	0.14	0.13	0.15	70	1071902	417	55	353	9	488
3ZND_W	tRNA links to Rfam database...	0.50	0.48	0.52	11	2982	13	0	10	3	12
4A1C_3	5S_rRNA links to Rfam database...	0.23	0.20	0.28	11	7101	28	2	26	0	43
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.09	0.08	3	11741	46	10	27	9	30
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 Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

2. Individual counts for Sfold [ 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 ]