CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CentroidAlifold(20)		RNAfold
MCC	0.726	>	0.396
Average MCC ± 95% Confidence Intervals	0.718 ± 0.036	>	0.398 ± 0.029
Sensitivity	0.614	>	0.398
Positive Predictive Value	0.860	>	0.394
Total TP	22679	>	14714
Total TN	104344087	>	104333103
Total FP	5560	<	25011
Total FP CONTRA	629	<	3719
Total FP INCONS	3071	<	18930
Total FP COMP	1860	<	2362
Total FN	14285	<	22250
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of CentroidAlifold(20) and RNAfold. 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 CentroidAlifold(20) and RNAfold).
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 CentroidAlifold(20) and RNAfold).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(20) and RNAfold. 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 CentroidAlifold(20) and RNAfold).

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

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

Total Base Pair Counts
Total TP	22679
Total TN	104344087
Total FP	5560
Total FP CONTRA	629
Total FP INCONS	3071
Total FP COMP	1860
Total FN	14285

Total Scores
MCC	0.726
Average MCC ± 95% Confidence Intervals	0.718 ± 0.036
Sensitivity	0.614
Positive Predictive Value	0.860
Nr of predictions	77

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2. Individual counts for CentroidAlifold(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...	0.91	0.86	0.95	394	1085188	51	6	13	32	64
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.83	0.77	0.90	365	1141911	54	9	31	14	109
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.93	374	1170812	45	10	19	16	96
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.93	364	1107423	43	10	19	14	92
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.85	0.78	0.93	368	1172351	42	9	18	15	105
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.92	380	1181542	47	10	21	16	96
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.91	365	1108906	48	11	23	14	92
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.86	0.78	0.95	363	1178497	43	4	16	23	102
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.92	372	1135875	46	11	20	15	91
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.85	0.78	0.93	371	1201625	47	10	19	18	105
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.92	372	1152515	48	10	24	14	94
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.91	364	1180015	52	13	24	15	107
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.86	0.78	0.94	364	1190809	45	4	19	22	104
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.80	0.75	0.86	332	1082272	67	11	41	15	113
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.83	0.75	0.92	356	1178493	48	7	24	17	117
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.86	0.79	0.94	377	1207832	45	8	18	19	98
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.86	0.79	0.94	378	1198524	39	8	16	15	100
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.93	367	1105932	46	9	20	17	86
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.85	0.77	0.92	375	1218735	46	11	20	15	109
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.92	370	1198524	46	11	21	14	108
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.91	360	1192345	51	10	25	16	108
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.92	362	1111893	46	11	20	15	93
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.91	355	1122363	48	8	25	15	107
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.86	0.79	0.92	354	1085218	46	8	21	17	92
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.93	371	1114870	46	9	21	16	86
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.85	0.78	0.91	354	1110408	50	12	21	17	99
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.84	0.78	0.91	351	1129869	54	7	29	18	99
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.92	357	1180030	50	8	21	21	107
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.89	357	1117860	63	9	34	20	96
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.92	357	1144951	49	9	24	16	107
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.91	350	1131377	50	7	26	17	106
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.83	0.77	0.90	353	1117869	56	11	27	18	105
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.82	0.75	0.91	356	1189260	53	9	28	16	120
CRW_00298	SSU_rRNA_eukarya links to Rfam database...	0.52	0.37	0.72	183	1620647	90	6	64	20	311
CRW_00301	SSU_rRNA_eukarya links to Rfam database...	0.47	0.34	0.64	178	1762223	133	11	91	31	341
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.52	0.37	0.73	171	1445616	97	6	57	34	291
CRW_00310	SSU_rRNA_eukarya links to Rfam database...	0.49	0.37	0.66	192	1805657	126	13	88	25	329
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.57	0.40	0.80	201	1627859	78	6	44	28	301
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.51	0.37	0.71	190	1988747	113	10	68	35	327
CRW_00332	SSU_rRNA_eukarya links to Rfam database...	0.48	0.34	0.67	161	1769781	123	8	71	44	316
CRW_00333	SSU_rRNA_eukarya links to Rfam database...	0.43	0.30	0.61	155	1892229	131	20	81	30	359
CRW_00345	SSU_rRNA_eukarya links to Rfam database...	0.51	0.36	0.72	181	1586621	96	8	61	27	317
CRW_00346	SSU_rRNA_eukarya links to Rfam database...	0.53	0.38	0.74	192	1584829	102	6	63	33	309
CRW_00348	SSU_rRNA_eukarya links to Rfam database...	0.54	0.40	0.72	200	1615226	107	10	67	30	303
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.53	0.39	0.73	196	1675098	99	8	63	28	311
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.52	0.37	0.71	180	1579501	100	8	64	28	302
CRW_00370	SSU_rRNA_eukarya links to Rfam database...	0.58	0.41	0.83	208	1640515	64	4	39	21	298
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.55	0.40	0.75	199	1611646	93	8	57	28	297
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.50	0.37	0.69	182	1626042	112	11	71	30	316
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.49	0.33	0.72	176	2126710	109	5	62	42	358
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.51	0.35	0.73	182	1751006	96	7	61	28	333
CRW_00403	SSU_rRNA_eukarya links to Rfam database...	0.52	0.39	0.70	180	1606270	126	11	67	48	284
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.51	0.38	0.68	189	1615224	117	8	82	27	307
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.48	0.34	0.67	170	1665972	109	11	72	26	325
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.86	0.79	0.93	364	1116372	45	9	20	16	94
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.86	0.78	0.94	347	1094091	45	2	20	23	98
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.86	0.79	0.93	359	1119369	53	3	25	25	93
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.86	0.79	0.92	354	1098520	55	6	23	26	92
CRW_00598	SSU_rRNA_eukarya links to Rfam database...	0.49	0.34	0.70	169	1665982	103	5	69	29	322
CRW_00758	SSU_rRNA_eukarya links to Rfam database...	0.52	0.38	0.72	184	1640510	108	6	66	36	299
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.51	0.38	0.69	181	1636884	113	8	72	33	300
CRW_00760	SSU_rRNA_eukarya links to Rfam database...	0.52	0.37	0.74	180	1638713	102	7	55	40	306
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.79	0.73	0.85	295	945652	81	5	48	28	109
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.83	0.76	0.91	340	1137411	63	5	30	28	107
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.80	0.72	0.88	284	1152598	97	3	36	58	110
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.82	0.76	0.88	357	1117854	65	10	39	16	113
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.91	369	1135873	50	13	23	14	95
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.50	0.36	0.69	179	1606270	108	8	71	29	324
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.49	0.36	0.67	183	1593733	116	11	78	27	323
CRW_01300	SSU_rRNA_eukarya links to Rfam database...	0.55	0.40	0.76	205	1693451	88	6	58	24	310
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.81	0.70	0.92	348	1073468	55	8	21	26	147
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.77	0.65	0.90	348	1500393	73	4	33	36	187
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.75	0.62	0.90	341	1471090	76	2	37	37	206
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.77	0.64	0.92	361	1606134	59	8	25	26	201
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.78	0.66	0.92	359	1433581	59	2	29	28	181
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.79	0.68	0.92	357	1204739	53	7	25	21	170
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.80	0.69	0.91	341	1117886	62	6	27	29	150

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Performance of RNAfold - scored lower in this pairwise comparison

1. Total counts & total scores for RNAfold

Total Base Pair Counts
Total TP	14714
Total TN	104333103
Total FP	25011
Total FP CONTRA	3719
Total FP INCONS	18930
Total FP COMP	2362
Total FN	22250

Total Scores
MCC	0.396
Average MCC ± 95% Confidence Intervals	0.398 ± 0.029
Sensitivity	0.398
Positive Predictive Value	0.394
Nr of predictions	77

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2. Individual counts for RNAfold [ 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	0.79	350	1085158	132	17	76	39	108
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.63	0.63	0.63	300	1141838	201	31	147	23	174
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.35	0.35	0.36	164	1170755	315	33	263	19	306
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.53	0.52	0.54	238	1107379	215	34	165	16	218
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.60	0.60	0.61	283	1172280	205	23	160	22	190
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.53	0.53	0.53	252	1181474	240	37	190	13	224
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.46	0.46	0.46	210	1108845	266	27	223	16	247
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.47	0.47	0.47	220	1178412	266	29	219	18	245
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.59	0.58	0.59	270	1135819	209	32	157	20	193
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.59	0.58	0.61	277	1201568	204	13	167	24	199
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.39	0.38	0.39	179	1152463	296	36	243	17	287
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.54	0.53	0.55	249	1179962	229	32	173	24	222
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.47	0.46	0.47	217	1190733	262	26	220	16	251
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.29	0.29	0.29	131	1082204	330	37	284	9	314
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.42	0.42	0.42	197	1178408	288	34	241	13	276
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.44	0.44	0.44	208	1207762	286	29	236	21	267
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.56	0.54	0.57	259	1198471	217	29	167	21	219
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.39	0.39	0.39	176	1105876	287	34	242	11	277
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.57	0.57	0.58	276	1218664	233	24	177	32	208
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.40	0.40	0.40	190	1198454	296	51	231	14	288
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.41	0.41	0.42	190	1192286	279	40	224	15	278
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.38	0.37	0.40	170	1111856	279	38	222	19	285
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.49	0.48	0.50	224	1122302	241	35	190	16	238
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.55	0.54	0.55	240	1085168	217	29	164	24	206
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.50	0.49	0.51	226	1114829	235	24	192	19	231
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.37	0.37	0.37	169	1110340	304	41	245	18	284
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.42	0.41	0.43	186	1129828	264	31	211	22	264
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.35	0.34	0.35	157	1179973	303	36	250	17	307
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.50	0.49	0.50	222	1117818	233	28	192	13	231
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.30	0.30	0.29	138	1144872	346	41	290	15	326
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.28	0.27	0.28	124	1131316	333	36	284	13	332
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.63	0.62	0.63	284	1117810	186	24	142	20	174
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.39	0.38	0.40	181	1189200	291	36	236	19	295
CRW_00298	SSU_rRNA_eukarya links to Rfam database...	0.17	0.18	0.16	88	1620349	501	88	375	38	406
CRW_00301	SSU_rRNA_eukarya links to Rfam database...	0.30	0.31	0.29	160	1761955	447	75	313	59	359
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.26	0.26	0.25	121	1445372	410	63	294	53	341
CRW_00310	SSU_rRNA_eukarya links to Rfam database...	0.26	0.27	0.25	143	1805381	466	88	338	40	378
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.38	0.38	0.37	190	1627600	364	68	252	44	312
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.31	0.32	0.30	165	1988473	454	70	307	77	352
CRW_00332	SSU_rRNA_eukarya links to Rfam database...	0.24	0.25	0.22	121	1769478	461	108	314	39	356
CRW_00333	SSU_rRNA_eukarya links to Rfam database...	0.33	0.33	0.32	171	1891953	432	77	284	71	343
CRW_00345	SSU_rRNA_eukarya links to Rfam database...	0.35	0.36	0.33	181	1586320	404	77	293	34	317
CRW_00346	SSU_rRNA_eukarya links to Rfam database...	0.31	0.32	0.29	162	1584535	419	78	315	26	339
CRW_00348	SSU_rRNA_eukarya links to Rfam database...	0.24	0.24	0.24	123	1614984	435	64	332	39	380
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.39	0.39	0.38	199	1674839	381	67	260	54	308
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.35	0.36	0.33	174	1579233	393	84	262	47	308
CRW_00370	SSU_rRNA_eukarya links to Rfam database...	0.26	0.27	0.25	136	1640229	442	80	321	41	370
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.33	0.33	0.32	166	1611391	395	72	281	42	330
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.35	0.36	0.35	181	1625783	379	70	272	37	317
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.42	0.43	0.41	227	2126398	426	63	265	98	307
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.25	0.27	0.24	137	1750683	473	87	349	37	378
CRW_00403	SSU_rRNA_eukarya links to Rfam database...	0.31	0.33	0.29	154	1606000	439	76	298	65	310
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.33	0.34	0.32	169	1614974	406	78	282	46	327
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.28	0.29	0.27	143	1665688	437	80	314	43	352
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.61	0.59	0.62	272	1116326	195	24	143	28	186
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.18	0.18	0.18	78	1094024	373	34	324	15	367
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.31	0.31	0.31	138	1119315	322	37	266	19	314
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.37	0.38	0.37	168	1098447	302	42	246	14	278
CRW_00598	SSU_rRNA_eukarya links to Rfam database...	0.34	0.36	0.33	177	1665684	417	76	288	53	314
CRW_00758	SSU_rRNA_eukarya links to Rfam database...	0.28	0.29	0.27	142	1640237	420	85	302	33	341
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.21	0.22	0.20	105	1636621	473	79	340	54	376
CRW_00760	SSU_rRNA_eukarya links to Rfam database...	0.29	0.29	0.29	143	1638460	405	76	276	53	343
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.25	0.24	0.25	98	945608	317	41	253	23	306
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.36	0.36	0.36	161	1137337	307	44	244	19	286
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.22	0.23	0.21	89	1152504	360	53	275	32	305
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.48	0.48	0.48	225	1117795	263	20	220	23	245
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.62	0.61	0.62	282	1135826	195	25	145	25	182
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.30	0.30	0.30	149	1606023	407	50	306	51	354
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.26	0.27	0.25	136	1593470	434	80	319	35	370
CRW_01300	SSU_rRNA_eukarya links to Rfam database...	0.33	0.34	0.33	176	1693179	406	78	287	41	339
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.48	0.46	0.51	228	1073395	247	19	203	25	267
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.52	0.51	0.53	274	1500261	287	30	213	44	261
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.37	0.36	0.38	196	1470957	345	47	270	28	351
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.54	0.52	0.55	295	1605991	270	35	207	28	267
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.48	0.47	0.49	254	1433456	289	27	234	28	286
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.45	0.43	0.47	228	1204646	269	31	223	15	299
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.49	0.47	0.50	232	1117800	256	26	202	28	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 CentroidAlifold(20) - scored higher in this pairwise comparison

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

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

Performance of RNAfold - scored lower in this pairwise comparison

1. Total counts & total scores for RNAfold

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