CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CentroidFold		RSpredict(20)
MCC	0.492	>	0.470
Average MCC ± 95% Confidence Intervals	0.493 ± 0.028	>	0.478 ± 0.067
Sensitivity	0.430	>	0.423
Positive Predictive Value	0.563	>	0.523
Total TP	15655	>	15416
Total TN	102215715	>	102214042
Total FP	14303	<	16076
Total FP CONTRA	1836	<	2354
Total FP INCONS	10307	<	11701
Total FP COMP	2160	>	2021
Total FN	20775	<	21014
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of CentroidFold and RSpredict(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 CentroidFold and RSpredict(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 CentroidFold and RSpredict(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidFold and RSpredict(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 CentroidFold and RSpredict(20)).

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Performance of CentroidFold - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidFold

Total Base Pair Counts
Total TP	15655
Total TN	102215715
Total FP	14303
Total FP CONTRA	1836
Total FP INCONS	10307
Total FP COMP	2160
Total FN	20775

Total Scores
MCC	0.492
Average MCC ± 95% Confidence Intervals	0.493 ± 0.028
Sensitivity	0.430
Positive Predictive Value	0.563
Nr of predictions	76

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2. Individual counts for CentroidFold [ 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...	0.79	0.76	0.83	347	1085183	108	8	63	37	111
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.68	0.66	0.71	312	1141875	159	19	110	30	162
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.60	0.49	0.75	230	1170907	91	8	70	13	240
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.56	0.49	0.64	223	1107466	140	16	111	13	233
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.60	0.51	0.71	241	1172408	111	9	88	14	232
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.64	0.57	0.72	269	1181581	110	23	80	7	207
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.55	0.49	0.63	225	1108945	147	19	116	12	232
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.56	0.49	0.63	228	1178519	155	15	118	22	237
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.59	0.49	0.70	226	1135957	106	11	84	11	237
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.63	0.56	0.70	268	1201642	136	16	99	21	208
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.55	0.47	0.66	217	1152591	126	17	96	13	249
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.51	0.42	0.62	200	1180095	129	14	107	8	271
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.61	0.53	0.70	247	1190845	120	6	98	16	221
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.35	0.31	0.39	139	1082299	226	23	195	8	306
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.52	0.45	0.59	213	1178522	162	17	128	17	260
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.59	0.52	0.67	247	1207869	131	18	101	12	228
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.59	0.52	0.67	250	1198552	140	19	105	16	228
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.56	0.49	0.65	221	1105989	128	13	105	10	232
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.66	0.61	0.71	296	1218724	154	20	101	33	188
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.57	0.50	0.66	237	1198568	130	20	101	9	241
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.45	0.35	0.57	165	1192449	145	20	106	19	303
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.67	0.57	0.79	260	1111955	83	11	60	12	195
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.48	0.41	0.55	190	1122405	171	26	130	15	272
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.51	0.43	0.60	194	1085280	142	14	113	15	252
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.62	0.54	0.70	249	1114913	130	13	96	21	208
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.48	0.36	0.64	165	1110536	105	15	79	11	288
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.49	0.41	0.57	186	1129931	157	13	126	18	264
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.54	0.45	0.64	209	1180088	132	19	100	13	255
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.53	0.42	0.67	192	1117973	105	9	86	10	261
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.62	0.57	0.68	265	1144950	146	18	108	20	199
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.48	0.36	0.65	162	1131511	101	11	76	14	294
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.67	0.59	0.76	268	1117909	98	16	67	15	190
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.61	0.55	0.68	260	1189270	143	18	105	20	216
CRW_00298	SSU_rRNA_eukarya links to Rfam database...	0.25	0.22	0.28	109	1620517	295	50	224	21	385
CRW_00301	SSU_rRNA_eukarya links to Rfam database...	0.48	0.39	0.58	203	1762152	211	28	120	63	316
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.29	0.26	0.32	120	1445480	309	50	200	59	342
CRW_00310	SSU_rRNA_eukarya links to Rfam database...	0.38	0.34	0.42	178	1805524	303	44	204	55	343
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.57	0.48	0.67	240	1627752	163	19	99	45	262
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.30	0.25	0.36	131	1988654	302	33	197	72	386
CRW_00332	SSU_rRNA_eukarya links to Rfam database...	0.25	0.22	0.28	104	1769656	299	47	214	38	373
CRW_00333	SSU_rRNA_eukarya links to Rfam database...	0.30	0.24	0.36	125	1892139	288	29	192	67	389
CRW_00345	SSU_rRNA_eukarya links to Rfam database...	0.41	0.37	0.45	186	1586456	267	40	189	38	312
CRW_00346	SSU_rRNA_eukarya links to Rfam database...	0.40	0.38	0.42	189	1584645	289	48	208	33	312
CRW_00348	SSU_rRNA_eukarya links to Rfam database...	0.37	0.31	0.44	157	1615148	235	27	171	37	346
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.42	0.39	0.45	200	1674917	285	39	209	37	307
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.34	0.31	0.38	150	1579355	289	44	204	41	332
CRW_00370	SSU_rRNA_eukarya links to Rfam database...	0.38	0.33	0.43	167	1640375	256	43	181	32	339
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.47	0.39	0.56	194	1611562	196	29	125	42	302
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.48	0.41	0.58	202	1625955	204	26	123	55	296
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.32	0.30	0.34	156	1750800	337	47	253	37	359
CRW_00403	SSU_rRNA_eukarya links to Rfam database...	0.31	0.29	0.34	135	1606132	324	52	209	63	329
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.42	0.35	0.49	173	1615153	226	27	150	49	323
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.42	0.36	0.48	180	1665851	239	34	160	45	315
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.71	0.64	0.79	292	1116394	100	14	65	21	166
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.34	0.28	0.42	125	1094162	188	16	157	15	320
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.37	0.32	0.43	143	1119420	207	36	157	14	309
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.65	0.59	0.72	261	1098541	124	19	82	23	185
CRW_00598	SSU_rRNA_eukarya links to Rfam database...	0.40	0.37	0.45	180	1665823	270	42	180	48	311
CRW_00758	SSU_rRNA_eukarya links to Rfam database...	0.37	0.34	0.40	164	1640353	298	41	208	49	319
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.34	0.28	0.42	134	1636828	232	34	149	49	347
CRW_00760	SSU_rRNA_eukarya links to Rfam database...	0.38	0.34	0.42	167	1638559	278	50	179	49	319
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.38	0.30	0.50	120	945758	137	16	106	15	284
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.51	0.40	0.65	179	1137510	120	5	92	23	268
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.35	0.28	0.44	110	1152672	173	15	124	34	284
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.59	0.56	0.62	265	1117830	190	14	151	25	205
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.63	0.55	0.72	256	1135921	119	15	86	18	208
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.41	0.37	0.45	185	1606114	268	39	190	39	318
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.46	0.41	0.52	206	1593608	228	40	151	37	300
CRW_01300	SSU_rRNA_eukarya links to Rfam database...	0.41	0.37	0.45	192	1693289	291	56	183	52	323
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.55	0.49	0.61	244	1073448	180	13	140	27	251
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.53	0.49	0.57	264	1500316	234	15	183	36	271
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.46	0.39	0.55	215	1471076	203	25	154	24	332
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.57	0.53	0.61	297	1606045	214	20	166	28	265
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.62	0.57	0.68	307	1433517	177	8	139	30	233
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.49	0.42	0.59	220	1204752	177	19	137	21	307
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.51	0.47	0.56	229	1117849	211	14	168	29	262

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

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

Total Base Pair Counts
Total TP	15416
Total TN	102214042
Total FP	16076
Total FP CONTRA	2354
Total FP INCONS	11701
Total FP COMP	2021
Total FN	21014

Total Scores
MCC	0.470
Average MCC ± 95% Confidence Intervals	0.478 ± 0.067
Sensitivity	0.423
Positive Predictive Value	0.523
Nr of predictions	76

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2. Individual counts for RSpredict(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...	0.78	0.76	0.80	349	1085166	117	16	70	31	109
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.60	0.50	0.71	239	1141980	119	16	81	22	235
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.74	0.71	0.78	332	1170788	124	21	74	29	138
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.72	0.68	0.76	308	1107412	121	17	79	25	148
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.73	0.68	0.78	320	1172336	118	19	71	28	153
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.63	0.55	0.72	260	1181590	123	18	85	20	216
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.73	0.69	0.77	314	1108895	119	18	78	23	143
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.73	0.69	0.78	320	1178470	123	16	74	33	145
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.73	0.68	0.79	316	1135876	116	15	71	30	147
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.72	0.67	0.77	320	1201607	124	19	79	26	156
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.73	0.68	0.79	315	1152520	110	20	66	24	151
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.71	0.65	0.77	308	1180015	120	17	76	27	163
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.73	0.68	0.79	317	1190796	115	15	68	32	151
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.68	0.63	0.74	281	1082274	126	20	81	25	164
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.66	0.60	0.74	283	1178495	122	22	80	20	190
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.71	0.67	0.76	316	1207819	125	23	77	25	159
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.72	0.67	0.77	319	1198513	119	20	74	25	159
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.70	0.63	0.78	285	1105963	105	14	66	25	168
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.71	0.67	0.76	322	1218719	127	19	81	27	162
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.72	0.66	0.78	317	1198517	119	19	73	27	161
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.71	0.62	0.81	292	1192380	91	18	50	23	176
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.68	0.60	0.77	272	1111934	101	13	67	21	183
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.70	0.65	0.75	301	1122349	125	21	80	24	161
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.67	0.60	0.76	266	1085250	106	16	69	21	180
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.73	0.69	0.77	315	1114864	116	18	74	24	142
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.62	0.54	0.71	244	1110451	120	17	83	20	209
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.60	0.51	0.71	231	1129930	115	14	81	20	219
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.71	0.66	0.75	308	1180005	131	20	83	28	156
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.71	0.66	0.75	300	1117861	125	19	80	26	153
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.72	0.67	0.77	311	1144937	123	15	78	30	153
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.71	0.66	0.77	301	1131370	113	18	71	24	155
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.64	0.55	0.73	254	1117913	115	15	78	22	204
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.70	0.66	0.76	312	1189241	126	19	81	26	164
CRW_00298	SSU_rRNA_eukarya links to Rfam database...	0.01	0.01	0.01	3	1620508	410	63	326	21	491
CRW_00301	SSU_rRNA_eukarya links to Rfam database...	0.33	0.31	0.36	161	1762053	322	46	243	33	358
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.37	0.34	0.39	158	1445446	293	34	212	47	304
CRW_00310	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1805520	442	63	359	20	513
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.36	0.34	0.38	172	1627656	314	50	232	32	330
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1988575	477	82	350	45	509
CRW_00332	SSU_rRNA_eukarya links to Rfam database...	0.01	0.01	0.01	3	1769654	389	59	305	25	474
CRW_00333	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	1	1892051	454	80	353	21	513
CRW_00345	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1586488	384	57	318	9	490
CRW_00346	SSU_rRNA_eukarya links to Rfam database...	0.35	0.31	0.39	156	1584690	293	33	211	49	345
CRW_00348	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1615104	410	69	330	11	503
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1674979	406	62	324	20	507
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.01	0.01	0.01	4	1579393	371	66	290	15	478
CRW_00370	SSU_rRNA_eukarya links to Rfam database...	0.39	0.37	0.42	186	1640327	297	32	221	44	320
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1611495	424	63	344	17	488
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1625926	390	51	321	18	490
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1750835	427	65	348	14	507
CRW_00403	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1606168	385	68	292	25	464
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1615135	382	74	294	14	496
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.33	0.31	0.36	152	1665808	305	45	220	40	343
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.64	0.56	0.73	258	1116413	115	15	79	21	200
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.64	0.55	0.75	244	1094136	105	9	71	25	201
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.63	0.55	0.73	249	1119415	115	6	86	23	203
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.70	0.63	0.76	283	1098533	118	13	74	31	163
CRW_00598	SSU_rRNA_eukarya links to Rfam database...	0.30	0.27	0.33	134	1665821	312	37	233	42	357
CRW_00758	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1640340	444	79	347	18	483
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	9	1636732	429	64	340	25	472
CRW_00760	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1638553	425	77	325	23	486
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.59	0.49	0.71	196	945723	109	10	71	28	208
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.65	0.57	0.75	254	1137446	113	13	73	27	193
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.63	0.53	0.75	209	1152644	114	10	58	46	185
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.61	0.51	0.72	241	1117925	111	14	80	17	229
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.73	0.69	0.77	319	1135862	125	18	79	28	145
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.35	0.31	0.40	155	1606145	262	44	184	34	348
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.02	0.01	0.02	7	1593610	403	61	327	15	499
CRW_01300	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1693285	445	62	373	10	515
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.67	0.60	0.75	297	1073447	132	13	88	31	198
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.62	0.50	0.76	266	1500430	124	10	72	42	269
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.62	0.49	0.77	268	1471123	123	8	71	44	279
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.63	0.49	0.80	278	1606180	104	12	58	34	284
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.61	0.50	0.75	270	1433609	124	8	84	32	270
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.64	0.54	0.76	282	1204758	129	8	80	41	245
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.69	0.62	0.77	305	1117865	121	14	76	31	186

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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 CentroidFold - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidFold

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

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

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

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