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)		Contrafold
MCC	0.674	>	0.477
Average MCC ± 95% Confidence Intervals	0.674 ± 0.044	>	0.480 ± 0.027
Sensitivity	0.621	>	0.461
Positive Predictive Value	0.732	>	0.494
Total TP	22941	>	17036
Total TN	104339145	>	104335974
Total FP	9959	<	20448
Total FP CONTRA	1517	<	2637
Total FP INCONS	6863	<	14819
Total FP COMP	1579	<	2992
Total FN	14023	<	19928
P-value	3.56938820447e-08

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Performance plots

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

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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	22941
Total TN	104339145
Total FP	9959
Total FP CONTRA	1517
Total FP INCONS	6863
Total FP COMP	1579
Total FN	14023

Total Scores
MCC	0.674
Average MCC ± 95% Confidence Intervals	0.674 ± 0.044
Sensitivity	0.621
Positive Predictive Value	0.732
Nr of predictions	77

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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_00034	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.87	371	1141890	74	12	43	19	103
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_00306	SSU_rRNA_eukarya links to Rfam database...	0.42	0.38	0.46	176	1445467	237	39	168	30	286
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_00346	SSU_rRNA_eukarya links to Rfam database...	0.45	0.40	0.50	202	1584688	230	32	168	30	299
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_00997	SSU_rRNA_bacteria links to Rfam database...	0.84	0.81	0.88	374	1135854	61	12	38	11	90
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 Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	17036
Total TN	104335974
Total FP	20448
Total FP CONTRA	2637
Total FP INCONS	14819
Total FP COMP	2992
Total FN	19928

Total Scores
MCC	0.477
Average MCC ± 95% Confidence Intervals	0.480 ± 0.027
Sensitivity	0.461
Positive Predictive Value	0.494
Nr of predictions	77

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2. Individual counts for Contrafold [ 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...	0.77	0.77	0.78	351	1085153	140	12	85	43	107
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.68	0.68	0.68	320	1141844	188	22	130	36	154
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.60	0.57	0.64	268	1170795	174	25	127	22	202
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.54	0.52	0.56	237	1107395	202	25	159	18	219
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.64	0.60	0.67	286	1172318	164	20	122	22	187
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.59	0.58	0.61	274	1181504	188	29	146	13	202
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.51	0.51	0.53	231	1108865	226	32	177	17	226
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.55	0.53	0.57	245	1178450	213	19	166	28	220
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.56	0.52	0.61	243	1135878	175	14	143	18	220
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.62	0.60	0.64	287	1201577	192	19	142	31	189
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.55	0.51	0.59	237	1152519	185	22	143	20	229
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.53	0.49	0.57	233	1180006	196	22	155	19	238
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.62	0.59	0.64	277	1190763	182	19	137	26	191
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.34	0.34	0.35	150	1082228	288	32	246	10	295
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.50	0.48	0.52	228	1178444	227	20	188	19	245
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.57	0.55	0.59	259	1207798	197	27	151	19	216
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.54	0.52	0.56	250	1198476	220	27	173	20	228
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.53	0.51	0.55	229	1105912	212	23	164	25	224
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.64	0.62	0.66	301	1218683	200	21	136	43	183
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.58	0.56	0.61	267	1198490	184	24	145	15	211
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.47	0.44	0.50	206	1192327	232	26	181	25	262
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.66	0.63	0.69	286	1111874	157	20	106	31	169
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.51	0.48	0.53	221	1122337	215	30	163	22	241
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.47	0.46	0.49	203	1085190	233	20	188	25	243
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.61	0.59	0.63	271	1114843	186	19	138	29	186
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.44	0.40	0.49	182	1110423	203	23	167	13	271
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.44	0.42	0.47	190	1129849	240	28	189	23	260
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.60	0.56	0.64	262	1180004	173	25	125	23	202
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.55	0.51	0.60	232	1117873	173	15	140	18	221
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.64	0.62	0.65	288	1144901	182	17	135	30	176
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.51	0.47	0.56	216	1131371	196	24	149	23	240
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.66	0.63	0.68	289	1117836	159	19	116	24	169
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.60	0.57	0.63	270	1189221	197	21	141	35	206
CRW_00298	SSU_rRNA_eukarya links to Rfam database...	0.25	0.25	0.25	122	1620403	431	72	303	56	372
CRW_00301	SSU_rRNA_eukarya links to Rfam database...	0.43	0.40	0.45	210	1762038	324	41	214	69	309
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.28	0.28	0.29	129	1445402	388	63	256	69	333
CRW_00310	SSU_rRNA_eukarya links to Rfam database...	0.36	0.35	0.37	184	1805456	377	53	257	67	337
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.50	0.49	0.51	246	1627630	284	52	182	50	256
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.33	0.32	0.33	166	1988512	422	56	281	85	351
CRW_00332	SSU_rRNA_eukarya links to Rfam database...	0.26	0.26	0.26	122	1769544	429	70	285	74	355
CRW_00333	SSU_rRNA_eukarya links to Rfam database...	0.38	0.36	0.41	183	1892040	342	42	220	80	331
CRW_00345	SSU_rRNA_eukarya links to Rfam database...	0.39	0.40	0.39	197	1586366	355	58	250	47	301
CRW_00346	SSU_rRNA_eukarya links to Rfam database...	0.40	0.40	0.39	202	1584577	358	54	257	47	299
CRW_00348	SSU_rRNA_eukarya links to Rfam database...	0.35	0.34	0.36	170	1615029	355	51	253	51	333
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.39	0.40	0.38	202	1674827	390	57	279	54	305
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.33	0.33	0.33	157	1579284	361	57	255	49	325
CRW_00370	SSU_rRNA_eukarya links to Rfam database...	0.37	0.37	0.37	189	1640256	363	64	257	42	317
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.44	0.41	0.46	205	1611467	295	42	196	57	291
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.41	0.40	0.42	198	1625830	342	48	230	64	300
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.43	0.42	0.44	223	2126443	372	38	249	85	311
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.28	0.30	0.27	152	1750697	447	70	337	40	363
CRW_00403	SSU_rRNA_eukarya links to Rfam database...	0.28	0.28	0.28	131	1606062	404	68	267	69	333
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.39	0.36	0.42	181	1615070	306	41	211	54	315
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.36	0.37	0.36	181	1665721	382	54	269	59	314
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.70	0.68	0.73	312	1116336	148	19	98	31	146
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.33	0.30	0.36	134	1094090	257	24	212	21	311
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.36	0.35	0.38	157	1119345	281	41	213	27	295
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.62	0.60	0.65	268	1098489	182	28	118	36	178
CRW_00598	SSU_rRNA_eukarya links to Rfam database...	0.39	0.39	0.40	193	1665739	354	59	234	61	298
CRW_00758	SSU_rRNA_eukarya links to Rfam database...	0.35	0.35	0.35	170	1640283	375	51	262	62	313
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.31	0.30	0.32	145	1636697	372	51	252	69	336
CRW_00760	SSU_rRNA_eukarya links to Rfam database...	0.37	0.36	0.37	176	1638485	358	65	229	64	310
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.40	0.37	0.44	148	945666	215	18	168	29	256
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.48	0.44	0.53	196	1137416	209	14	160	35	251
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.35	0.33	0.38	131	1152575	263	22	193	48	263
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.57	0.56	0.57	265	1117797	226	19	179	28	205
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.62	0.60	0.64	280	1135838	187	19	141	27	184
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.39	0.39	0.40	194	1606043	347	52	239	56	309
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.45	0.44	0.47	221	1593534	302	49	201	52	285
CRW_01300	SSU_rRNA_eukarya links to Rfam database...	0.38	0.37	0.38	193	1693217	355	53	257	45	322
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.53	0.50	0.56	246	1073403	229	19	177	33	249
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.50	0.49	0.52	264	1500266	296	25	223	48	271
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.46	0.43	0.49	236	1470988	271	34	212	25	311
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.55	0.54	0.56	301	1605989	279	31	207	41	261
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.58	0.56	0.60	303	1433467	242	16	185	41	237
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.49	0.44	0.55	232	1204703	216	20	173	23	295
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.49	0.47	0.51	232	1117807	258	16	205	37	259

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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 Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

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