CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAalifold(20)		Afold
MCC	0.676	>	0.410
Average MCC ± 95% Confidence Intervals	0.677 ± 0.045	>	0.413 ± 0.031
Sensitivity	0.622	>	0.410
Positive Predictive Value	0.735	>	0.411
Total TP	21818	>	14374
Total TN	99031246	>	99025973
Total FP	9357	<	23038
Total FP CONTRA	1422	<	3302
Total FP INCONS	6446	<	17283
Total FP COMP	1489	<	2453
Total FN	13245	<	20689
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RNAalifold(20) and Afold. 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 RNAalifold(20) and Afold).
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 RNAalifold(20) and Afold).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(20) and Afold. 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 RNAalifold(20) and Afold).

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Performance of RNAalifold(20) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	21818
Total TN	99031246
Total FP	9357
Total FP CONTRA	1422
Total FP INCONS	6446
Total FP COMP	1489
Total FN	13245

Total Scores
MCC	0.676
Average MCC ± 95% Confidence Intervals	0.677 ± 0.045
Sensitivity	0.622
Positive Predictive Value	0.735
Nr of predictions	73

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2. Individual counts for RNAalifold(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...	0.87	0.84	0.90	385	1085172	61	7	37	17	73
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.83	0.80	0.86	374	1170779	75	11	51	13	96
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.84	0.82	0.87	372	1107390	68	12	42	14	84
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.81	0.76	0.86	361	1172324	71	11	50	10	112
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.90	382	1181529	55	14	28	13	94
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.86	0.83	0.89	381	1108875	61	12	37	12	76
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.85	0.81	0.90	376	1178461	63	6	37	20	89
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.84	0.82	0.87	380	1135841	71	13	44	14	83
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.82	0.78	0.87	371	1201597	71	12	45	14	105
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.84	0.80	0.88	372	1152500	62	12	37	13	94
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.79	0.75	0.82	355	1179984	91	17	60	14	116
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.83	0.79	0.88	368	1190777	71	7	44	20	100
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.77	0.75	0.80	332	1082242	94	12	70	12	113
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.80	0.76	0.84	358	1178455	78	13	54	11	115
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.82	0.79	0.86	373	1207803	68	15	44	9	102
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.83	0.79	0.88	378	1198495	67	12	41	14	100
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.86	0.83	0.89	378	1105903	56	14	33	9	75
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.79	0.75	0.83	364	1218705	87	17	55	15	120
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.88	373	1198502	61	12	39	10	105
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.82	0.78	0.87	363	1192322	68	14	41	13	105
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.85	0.83	0.88	376	1111859	66	12	39	15	79
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.82	0.79	0.87	363	1122332	69	11	45	13	99
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.84	0.81	0.87	360	1085185	68	13	43	12	86
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.84	0.81	0.87	368	1114849	68	12	42	14	89
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.82	0.79	0.85	359	1110374	76	14	48	14	94
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.82	0.78	0.86	349	1129851	72	10	46	16	101
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.81	0.78	0.85	360	1179994	80	12	50	18	104
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.83	0.79	0.87	360	1117845	71	12	43	16	93
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.82	0.78	0.85	363	1144916	75	12	50	13	101
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.84	0.80	0.89	363	1131350	62	12	35	15	93
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.83	0.79	0.88	364	1117844	66	13	39	14	94
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.81	0.76	0.86	361	1189232	70	13	47	10	115
CRW_00298	SSU_rRNA_eukarya links to Rfam database...	0.43	0.38	0.49	187	1620517	224	43	153	28	307
CRW_00301	SSU_rRNA_eukarya links to Rfam database...	0.42	0.37	0.48	192	1762101	229	37	173	19	327
CRW_00310	SSU_rRNA_eukarya links to Rfam database...	0.46	0.39	0.55	204	1805579	190	29	138	23	317
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.41	0.35	0.47	178	1627730	219	36	166	17	324
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.40	0.35	0.47	182	1988624	243	35	174	34	335
CRW_00332	SSU_rRNA_eukarya links to Rfam database...	0.39	0.34	0.43	164	1769642	239	35	180	24	313
CRW_00333	SSU_rRNA_eukarya links to Rfam database...	0.34	0.29	0.40	150	1892114	241	34	187	20	364
CRW_00345	SSU_rRNA_eukarya links to Rfam database...	0.43	0.38	0.48	189	1586477	222	39	166	17	309
CRW_00348	SSU_rRNA_eukarya links to Rfam database...	0.43	0.38	0.48	190	1615106	228	41	166	21	313
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.43	0.38	0.49	192	1674972	227	34	167	26	315
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.39	0.34	0.45	166	1579381	248	30	176	42	316
CRW_00370	SSU_rRNA_eukarya links to Rfam database...	0.52	0.47	0.57	240	1640342	204	34	150	20	266
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.43	0.38	0.49	187	1611527	222	27	169	26	309
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.40	0.35	0.46	174	1625925	228	37	170	21	324
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.40	0.34	0.47	179	2126574	228	31	169	28	355
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.44	0.37	0.51	193	1750879	199	35	149	15	322
CRW_00403	SSU_rRNA_eukarya links to Rfam database...	0.39	0.37	0.42	170	1606127	272	38	193	41	294
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.43	0.39	0.48	191	1615105	227	43	164	20	305
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.38	0.35	0.41	171	1665811	266	36	207	23	324
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.84	0.81	0.86	373	1116333	74	11	48	15	85
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.86	0.81	0.91	361	1094062	61	7	30	24	84
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.89	358	1119354	70	6	38	26	94
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.87	0.83	0.91	368	1098500	61	9	26	26	78
CRW_00598	SSU_rRNA_eukarya links to Rfam database...	0.42	0.38	0.47	187	1665825	229	39	174	16	304
CRW_00758	SSU_rRNA_eukarya links to Rfam database...	0.48	0.43	0.53	210	1640373	205	34	149	22	273
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.42	0.38	0.48	182	1636762	232	39	162	31	299
CRW_00760	SSU_rRNA_eukarya links to Rfam database...	0.43	0.37	0.50	179	1638594	209	38	144	27	307
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.78	0.74	0.83	298	945642	94	6	54	34	106
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.82	0.78	0.87	348	1137388	80	6	44	30	99
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.74	0.70	0.79	276	1152572	131	10	63	58	118
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.78	0.74	0.82	350	1117832	97	13	65	19	120
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.47	0.42	0.53	210	1606133	216	27	158	31	293
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.44	0.38	0.50	193	1593619	210	32	161	17	313
CRW_01300	SSU_rRNA_eukarya links to Rfam database...	0.52	0.45	0.59	231	1693331	174	31	127	16	284
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.78	0.71	0.86	353	1073436	80	10	46	24	142
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.75	0.65	0.86	347	1500373	97	7	51	39	188
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.73	0.62	0.86	341	1471072	93	2	55	36	206
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.75	0.65	0.87	364	1606111	77	8	45	24	198
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.76	0.67	0.87	360	1433555	85	3	53	29	180
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.72	0.65	0.80	341	1204702	101	13	72	16	186
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.78	0.71	0.86	347	1117857	83	8	48	27	144

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Performance of Afold - scored lower in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP	14374
Total TN	99025973
Total FP	23038
Total FP CONTRA	3302
Total FP INCONS	17283
Total FP COMP	2453
Total FN	20689

Total Scores
MCC	0.410
Average MCC ± 95% Confidence Intervals	0.413 ± 0.031
Sensitivity	0.410
Positive Predictive Value	0.411
Nr of predictions	73

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2. Individual counts for Afold [ 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...	0.78	0.77	0.79	351	1085158	132	17	75	40	107
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.49	0.49	0.50	228	1170758	252	20	209	23	242
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.46	0.46	0.46	208	1107368	260	31	209	20	248
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.52	0.51	0.53	240	1172289	233	26	191	16	233
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.55	0.54	0.55	259	1181483	231	27	184	20	217
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.49	0.49	0.50	226	1108849	247	24	206	17	231
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.46	0.46	0.47	214	1178420	264	32	214	18	251
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.64	0.63	0.64	291	1135826	182	20	141	21	172
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.59	0.58	0.60	274	1201566	212	26	159	27	202
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.42	0.41	0.42	193	1152465	282	35	228	19	273
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.64	0.62	0.65	293	1179965	180	30	128	22	178
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.54	0.53	0.55	248	1190745	226	28	175	23	220
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.29	0.29	0.29	127	1082216	323	37	276	10	318
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.44	0.43	0.45	203	1178433	259	22	222	15	270
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.47	0.46	0.48	220	1207772	267	24	219	24	255
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.57	0.56	0.58	266	1198467	216	21	172	23	212
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.38	0.38	0.38	172	1105880	289	44	232	13	281
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.57	0.57	0.58	274	1218666	234	21	180	33	210
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.44	0.44	0.45	210	1198459	274	34	223	17	268
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.41	0.40	0.42	188	1192291	278	39	222	17	280
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.44	0.43	0.45	196	1111850	260	40	200	20	259
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.51	0.50	0.51	231	1122302	237	43	175	19	231
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.59	0.58	0.60	258	1085174	195	26	143	26	188
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.47	0.47	0.48	213	1114826	258	28	204	26	244
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.38	0.38	0.38	172	1110338	300	45	240	15	281
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.41	0.40	0.42	180	1129825	274	33	218	23	270
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.51	0.49	0.53	229	1179985	227	29	173	25	235
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.51	0.50	0.51	227	1117817	231	28	188	15	226
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.30	0.30	0.29	138	1144872	347	41	290	16	326
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.28	0.27	0.28	124	1131316	337	30	290	17	332
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.72	0.71	0.74	325	1117819	142	23	93	26	133
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.46	0.45	0.48	214	1189204	258	34	201	23	262
CRW_00298	SSU_rRNA_eukarya links to Rfam database...	0.19	0.20	0.18	99	1620353	490	81	367	42	395
CRW_00301	SSU_rRNA_eukarya links to Rfam database...	0.30	0.31	0.30	162	1761957	428	86	298	44	357
CRW_00310	SSU_rRNA_eukarya links to Rfam database...	0.29	0.30	0.28	157	1805386	453	81	326	46	364
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.41	0.41	0.42	204	1627621	339	47	238	54	298
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.32	0.32	0.31	167	1988474	452	69	305	78	350
CRW_00332	SSU_rRNA_eukarya links to Rfam database...	0.18	0.20	0.17	94	1769479	492	105	343	44	383
CRW_00333	SSU_rRNA_eukarya links to Rfam database...	0.29	0.30	0.28	153	1891946	449	74	312	63	361
CRW_00345	SSU_rRNA_eukarya links to Rfam database...	0.34	0.35	0.33	175	1586340	403	71	285	47	323
CRW_00348	SSU_rRNA_eukarya links to Rfam database...	0.25	0.25	0.24	127	1614982	437	68	326	43	376
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.36	0.36	0.35	183	1674845	391	61	276	54	324
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.35	0.36	0.33	174	1579230	395	88	261	46	308
CRW_00370	SSU_rRNA_eukarya links to Rfam database...	0.28	0.28	0.28	143	1640248	420	77	298	45	363
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.29	0.29	0.28	145	1611389	409	77	299	33	351
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.36	0.36	0.35	181	1625787	378	59	279	40	317
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.42	0.43	0.41	227	2126401	423	55	270	98	307
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.24	0.25	0.23	129	1750683	478	83	361	34	386
CRW_00403	SSU_rRNA_eukarya links to Rfam database...	0.31	0.31	0.30	146	1606035	431	65	282	84	318
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.34	0.34	0.34	169	1615006	381	62	266	53	327
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.27	0.28	0.26	140	1665694	436	77	314	45	355
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.60	0.59	0.62	268	1116330	196	21	146	29	190
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.18	0.18	0.18	78	1094024	374	34	324	16	367
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.36	0.36	0.37	161	1119326	290	30	239	21	291
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.57	0.56	0.59	251	1098476	205	23	153	29	195
CRW_00598	SSU_rRNA_eukarya links to Rfam database...	0.31	0.33	0.29	162	1665675	440	88	300	52	329
CRW_00758	SSU_rRNA_eukarya links to Rfam database...	0.29	0.30	0.29	144	1640268	416	66	288	62	339
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.22	0.22	0.21	107	1636633	462	78	327	57	374
CRW_00760	SSU_rRNA_eukarya links to Rfam database...	0.28	0.29	0.28	140	1638458	411	74	283	54	346
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.26	0.25	0.26	103	945610	313	37	250	26	301
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.36	0.36	0.36	160	1137342	302	44	240	18	287
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.21	0.22	0.21	85	1152511	379	51	274	54	309
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.49	0.48	0.49	227	1117798	259	23	212	24	243
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.32	0.32	0.32	160	1606024	390	54	290	46	343
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.32	0.33	0.31	167	1593473	402	81	284	37	339
CRW_01300	SSU_rRNA_eukarya links to Rfam database...	0.36	0.37	0.35	189	1693186	392	71	274	47	326
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.53	0.50	0.56	246	1073408	220	17	174	29	249
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.55	0.53	0.56	284	1500271	276	22	201	53	251
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.36	0.35	0.37	191	1470959	352	45	275	32	356
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.56	0.54	0.58	306	1605999	254	32	191	31	256
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.60	0.58	0.63	313	1433471	221	15	172	34	227
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.46	0.43	0.49	228	1204659	250	31	210	9	299
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.51	0.48	0.53	237	1117812	242	21	190	31	254

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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 RNAalifold(20) - scored higher in this pairwise comparison

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

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

Performance of Afold - scored lower in this pairwise comparison

1. Total counts & total scores for Afold

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