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		Carnac(20)
MCC	0.725	>	0.558
Average MCC ± 95% Confidence Intervals	0.730 ± 0.051	>	0.553 ± 0.023
Sensitivity	0.688	>	0.348
Positive Predictive Value	0.765	<	0.895
Total TP	25438	>	12872
Total TN	104337206	<	104356083
Total FP	9384	>	2613
Total FP CONTRA	1325	>	170
Total FP INCONS	6497	>	1341
Total FP COMP	1562	>	1102
Total FN	11526	<	24092
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of ContextFold and Carnac(20). 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 Carnac(20)).
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 Carnac(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and Carnac(20). 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 Carnac(20)).

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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	25438
Total TN	104337206
Total FP	9384
Total FP CONTRA	1325
Total FP INCONS	6497
Total FP COMP	1562
Total FN	11526

Total Scores
MCC	0.725
Average MCC ± 95% Confidence Intervals	0.730 ± 0.051
Sensitivity	0.688
Positive Predictive Value	0.765
Nr of predictions	77

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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
CRW_00024	SSU_rRNA_archaea links to Rfam database...	0.95	0.92	0.98	423	1085170	15	3	5	7	35
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.91	0.89	0.93	421	1141864	43	16	15	12	53
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.94	0.90	0.98	421	1170787	8	3	4	1	49
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.94	0.90	0.97	412	1107393	12	2	9	1	44
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.91	0.88	0.95	416	1172309	22	2	19	1	57
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.94	0.90	0.97	429	1181511	14	7	6	1	47
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.95	0.92	0.99	421	1108878	11	2	4	5	36
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.96	0.92	0.99	430	1178445	8	0	5	3	35
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.93	0.90	0.97	415	1135850	16	2	11	3	48
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.93	0.89	0.97	426	1201584	22	4	11	7	50
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.85	0.81	0.90	376	1152502	48	6	37	5	90
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.91	0.87	0.95	412	1179984	23	8	12	3	59
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.95	0.91	0.99	427	1190763	11	0	6	5	41
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.78	0.71	0.85	318	1082280	60	6	52	2	127
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.92	0.88	0.97	417	1178448	25	2	13	10	56
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.94	0.89	1.00	424	1207810	4	1	0	3	51
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.94	0.90	0.97	431	1198483	18	4	8	6	47
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.93	0.89	0.97	404	1105911	13	2	11	0	49
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.92	0.89	0.96	433	1218688	25	3	17	5	51
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.94	0.91	0.98	435	1198481	12	4	6	2	43
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.91	376	1192327	51	4	33	14	92
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.91	0.86	0.95	391	1111876	31	0	19	12	64
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.92	0.88	0.98	405	1122336	12	2	8	2	57
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.91	0.86	0.97	383	1085207	14	1	10	3	63
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.94	0.90	0.98	412	1114849	15	3	7	5	45
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.83	0.79	0.87	359	1110384	57	9	43	5	94
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.77	0.70	0.84	316	1129880	68	9	51	8	134
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.89	0.84	0.94	389	1180004	36	4	19	13	75
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.92	0.88	0.95	398	1117843	21	4	15	2	55
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.92	0.87	0.96	405	1144919	21	2	15	4	59
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.89	365	1131352	48	0	43	5	91
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.95	0.91	0.99	416	1117839	7	2	3	2	42
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.90	382	1189229	44	4	38	2	94
CRW_00298	SSU_rRNA_eukarya links to Rfam database...	0.38	0.35	0.41	173	1620475	275	37	215	23	321
CRW_00301	SSU_rRNA_eukarya links to Rfam database...	0.51	0.47	0.55	245	1762058	245	26	174	45	274
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.37	0.36	0.37	168	1445399	304	63	220	21	294
CRW_00310	SSU_rRNA_eukarya links to Rfam database...	0.49	0.47	0.52	243	1805487	271	31	189	51	278
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.58	0.54	0.63	271	1627677	194	30	132	32	231
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.47	0.45	0.49	232	1988538	308	45	200	63	285
CRW_00332	SSU_rRNA_eukarya links to Rfam database...	0.50	0.46	0.54	218	1769618	245	34	151	60	259
CRW_00333	SSU_rRNA_eukarya links to Rfam database...	0.36	0.33	0.40	171	1892055	315	40	219	56	343
CRW_00345	SSU_rRNA_eukarya links to Rfam database...	0.39	0.38	0.41	187	1586412	289	48	224	17	311
CRW_00346	SSU_rRNA_eukarya links to Rfam database...	0.36	0.34	0.38	172	1584635	308	55	228	25	329
CRW_00348	SSU_rRNA_eukarya links to Rfam database...	0.46	0.44	0.49	219	1615055	262	39	190	33	284
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.46	0.45	0.47	227	1674887	268	53	198	17	280
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.45	0.42	0.48	202	1579334	251	36	181	34	280
CRW_00370	SSU_rRNA_eukarya links to Rfam database...	0.37	0.35	0.39	176	1640316	302	35	239	28	330
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.56	0.53	0.58	263	1611460	230	33	154	43	233
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.47	0.45	0.49	225	1625846	264	44	191	29	273
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.62	0.59	0.65	314	2126472	237	36	131	70	220
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.39	0.38	0.39	197	1750754	338	55	250	33	318
CRW_00403	SSU_rRNA_eukarya links to Rfam database...	0.51	0.48	0.55	222	1606122	262	30	154	78	242
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.55	0.52	0.59	257	1615067	222	34	145	43	239
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.43	0.41	0.44	205	1665761	293	45	214	34	290
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.95	0.92	0.98	421	1116336	10	3	5	2	37
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.90	350	1094071	49	3	36	10	95
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	358	1119364	45	3	31	11	94
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.92	0.88	0.96	393	1098492	32	6	12	14	53
CRW_00598	SSU_rRNA_eukarya links to Rfam database...	0.31	0.29	0.34	144	1665799	323	40	242	41	347
CRW_00758	SSU_rRNA_eukarya links to Rfam database...	0.46	0.45	0.48	217	1640313	290	20	216	54	266
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.40	0.38	0.42	181	1636714	284	45	205	34	300
CRW_00760	SSU_rRNA_eukarya links to Rfam database...	0.41	0.39	0.43	189	1638513	310	51	202	57	297
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.71	0.65	0.79	262	945667	95	9	62	24	142
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.91	357	1137392	54	3	34	17	90
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.65	0.59	0.71	232	1152596	140	14	79	47	162
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.93	0.90	0.96	425	1117816	31	1	18	12	45
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.92	0.90	0.95	419	1135835	28	6	18	4	45
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.41	0.40	0.43	199	1606068	288	37	224	27	304
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.50	0.47	0.53	237	1593555	238	35	178	25	269
CRW_01300	SSU_rRNA_eukarya links to Rfam database...	0.38	0.36	0.40	185	1693252	309	52	231	26	330
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.87	0.79	0.96	392	1073435	37	4	14	19	103
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.90	0.85	0.95	455	1500298	52	7	18	27	80
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.85	0.78	0.93	426	1471011	64	4	29	31	121
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.86	0.81	0.91	455	1606027	68	3	43	22	107
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.90	0.85	0.96	459	1433493	36	3	16	17	81
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.88	0.80	0.97	422	1204693	33	2	11	20	105
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.86	0.78	0.94	385	1117852	50	4	19	27	106

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Performance of Carnac(20) - scored lower in this pairwise comparison

1. Total counts & total scores for Carnac(20)

Total Base Pair Counts
Total TP	12872
Total TN	104356083
Total FP	2613
Total FP CONTRA	170
Total FP INCONS	1341
Total FP COMP	1102
Total FN	24092

Total Scores
MCC	0.558
Average MCC ± 95% Confidence Intervals	0.553 ± 0.023
Sensitivity	0.348
Positive Predictive Value	0.895
Nr of predictions	77

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2. Individual counts for Carnac(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00024	SSU_rRNA_archaea links to Rfam database...	0.74	0.59	0.94	270	1085313	35	5	13	17	188
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.56	0.35	0.90	166	1142131	28	4	15	9	308
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.62	0.43	0.91	202	1170992	29	3	18	8	268
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.62	0.42	0.91	191	1107607	23	4	14	5	265
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.64	0.43	0.95	204	1172532	17	3	7	7	269
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.63	0.42	0.94	199	1181742	19	2	10	7	277
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.69	0.51	0.94	234	1109056	28	2	13	13	223
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.62	0.43	0.92	198	1178664	29	0	18	11	267
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.71	0.53	0.95	246	1136018	21	2	12	7	217
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.64	0.43	0.93	207	1201802	26	4	12	10	269
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.66	0.46	0.95	216	1152694	16	3	8	5	250
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.69	0.52	0.92	244	1180151	26	4	17	5	227
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.64	0.44	0.93	207	1190974	24	0	15	9	261
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.56	0.36	0.89	158	1082478	26	2	18	6	287
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.52	0.32	0.87	149	1178708	29	3	20	6	324
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.64	0.43	0.96	204	1208022	12	2	7	3	271
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.66	0.47	0.93	227	1198681	28	3	15	10	251
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.65	0.45	0.93	205	1106108	20	3	12	5	248
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.56	0.35	0.91	168	1218956	27	4	13	10	316
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.68	0.50	0.91	241	1198660	33	4	21	8	237
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.64	0.43	0.97	200	1192533	11	3	4	4	268
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.66	0.47	0.93	212	1112057	22	4	13	5	243
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.62	0.41	0.94	191	1122548	17	3	9	5	271
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.57	0.35	0.92	156	1085431	16	4	10	2	290
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.60	0.37	0.95	171	1115091	13	2	7	4	286
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.64	0.44	0.93	201	1110578	20	3	13	4	252
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.52	0.29	0.92	130	1130115	15	4	7	4	320
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.68	0.51	0.92	237	1180158	31	3	18	10	227
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.66	0.46	0.96	209	1118042	12	1	8	3	244
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.65	0.45	0.95	209	1145120	17	2	10	5	255
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.53	0.33	0.87	150	1131587	27	3	20	4	306
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.62	0.41	0.93	188	1118058	18	2	12	4	270
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.58	0.41	0.84	194	1189422	41	5	32	4	282
CRW_00298	SSU_rRNA_eukarya links to Rfam database...	0.41	0.19	0.86	95	1620790	37	0	15	22	399
CRW_00301	SSU_rRNA_eukarya links to Rfam database...	0.46	0.25	0.83	131	1762345	56	0	27	29	388
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.55	0.32	0.95	146	1445697	38	0	7	31	316
CRW_00310	SSU_rRNA_eukarya links to Rfam database...	0.42	0.22	0.81	116	1805806	46	5	23	18	405
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.45	0.23	0.92	113	1627987	32	1	9	22	389
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.34	0.17	0.67	89	1988883	69	3	40	26	428
CRW_00332	SSU_rRNA_eukarya links to Rfam database...	0.39	0.20	0.76	97	1769893	46	1	30	15	380
CRW_00333	SSU_rRNA_eukarya links to Rfam database...	0.35	0.17	0.70	88	1892359	50	4	34	12	426
CRW_00345	SSU_rRNA_eukarya links to Rfam database...	0.48	0.29	0.81	145	1586691	63	2	33	28	353
CRW_00346	SSU_rRNA_eukarya links to Rfam database...	0.47	0.28	0.79	138	1584915	66	1	36	29	363
CRW_00348	SSU_rRNA_eukarya links to Rfam database...	0.40	0.23	0.72	114	1615344	78	4	41	33	389
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.49	0.25	0.96	129	1675231	29	0	5	24	378
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.47	0.25	0.87	122	1579613	37	1	17	19	360
CRW_00370	SSU_rRNA_eukarya links to Rfam database...	0.47	0.27	0.84	135	1640605	54	1	25	28	371
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.48	0.29	0.81	143	1611733	59	1	33	25	353
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.44	0.23	0.84	117	1626166	46	2	21	23	381
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.49	0.26	0.93	140	2126802	50	1	10	39	394
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.30	0.13	0.71	67	1751161	53	2	26	25	448
CRW_00403	SSU_rRNA_eukarya links to Rfam database...	0.48	0.27	0.83	127	1606375	60	0	26	34	337
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.39	0.19	0.81	94	1615387	42	0	22	20	402
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.38	0.19	0.74	96	1666095	60	1	33	26	399
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.62	0.42	0.91	192	1116554	28	4	15	9	266
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.58	0.35	0.97	156	1094299	10	0	5	5	289
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.55	0.33	0.93	148	1119597	15	1	10	4	304
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.66	0.46	0.93	206	1098682	26	1	14	11	240
CRW_00598	SSU_rRNA_eukarya links to Rfam database...	0.42	0.20	0.85	100	1666107	41	0	18	23	391
CRW_00758	SSU_rRNA_eukarya links to Rfam database...	0.46	0.26	0.79	127	1640605	57	4	30	23	356
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.39	0.19	0.79	93	1637028	51	3	21	27	388
CRW_00760	SSU_rRNA_eukarya links to Rfam database...	0.45	0.24	0.84	117	1638815	55	0	23	32	369
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.48	0.30	0.77	122	945842	42	3	33	6	282
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.61	0.43	0.88	191	1137570	34	1	24	9	256
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.59	0.38	0.90	150	1152755	40	0	16	24	244
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.62	0.42	0.92	196	1118046	27	3	15	9	274
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.60	0.39	0.93	181	1136084	19	3	10	6	283
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.44	0.25	0.76	126	1606363	56	1	38	17	377
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.47	0.25	0.90	125	1593866	44	0	14	30	381
CRW_01300	SSU_rRNA_eukarya links to Rfam database...	0.47	0.25	0.88	128	1693575	38	0	17	21	387
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.60	0.40	0.92	196	1073633	28	3	13	12	299
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.62	0.41	0.95	218	1500548	29	3	9	17	317
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.59	0.38	0.92	206	1471246	35	2	16	17	341
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.62	0.40	0.96	226	1606292	20	3	7	10	336
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.58	0.36	0.94	192	1433767	24	1	11	12	348
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.62	0.41	0.93	216	1204895	30	4	13	13	311
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.66	0.48	0.92	234	1118007	37	4	15	18	257

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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 Carnac(20) - scored lower in this pairwise comparison

1. Total counts & total scores for Carnac(20)

2. Individual counts for Carnac(20) [ download as .csv ]