CompaRNA - on-line benchmarks of RNA structure prediction methods

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Overview

Metric	CentroidAlifold(seed)		Fold
MCC	0.796	>	0.412
Average MCC ± 95% Confidence Intervals	0.790 ± 0.032	>	0.411 ± 0.027
Sensitivity	0.706	>	0.413
Positive Predictive Value	0.897	>	0.411
Total TP	21223	>	12415
Total TN	79088671	>	79082106
Total FP	3503	<	19621
Total FP CONTRA	450	<	2495
Total FP INCONS	1983	<	15311
Total FP COMP	1070	<	1815
Total FN	8857	<	17665
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of CentroidAlifold(seed) and Fold. 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(seed) and Fold).
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(seed) and Fold).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(seed) and Fold. 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(seed) and Fold).

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

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

Total Base Pair Counts
Total TP	21223
Total TN	79088671
Total FP	3503
Total FP CONTRA	450
Total FP INCONS	1983
Total FP COMP	1070
Total FN	8857

Total Scores
MCC	0.796
Average MCC ± 95% Confidence Intervals	0.790 ± 0.032
Sensitivity	0.706
Positive Predictive Value	0.897
Nr of predictions	64

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2. Individual counts for CentroidAlifold(seed) [ 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...	0.90	0.86	0.95	393	1085187	55	6	15	34	65
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.90	368	1141906	52	10	32	10	106
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.93	385	1170801	38	9	20	9	85
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.93	374	1107413	39	9	20	10	82
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.92	372	1172342	41	9	23	9	101
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.92	381	1181541	41	9	22	10	95
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.93	375	1108900	39	9	21	9	82
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.87	0.80	0.93	373	1178481	41	4	22	15	92
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.92	379	1135867	41	9	23	9	84
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.93	381	1201614	41	9	21	11	95
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.93	372	1152519	39	9	21	9	94
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.93	376	1180010	40	9	21	10	95
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.94	374	1190796	41	4	22	15	94
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.82	0.76	0.88	340	1082268	59	9	39	11	105
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.84	0.78	0.91	368	1178477	47	9	26	12	105
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.93	383	1207823	39	9	20	10	92
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.93	381	1198515	40	9	21	10	97
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.93	372	1105927	39	9	20	10	81
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.85	0.78	0.92	379	1218731	41	9	22	10	105
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.92	382	1198513	40	9	22	9	96
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.93	374	1192336	40	9	21	10	94
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.93	373	1111883	39	9	21	9	82
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.90	358	1122354	48	8	31	9	104
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.86	0.81	0.92	361	1085207	41	8	25	8	85
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.92	371	1114869	40	9	22	9	86
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.90	363	1110392	50	13	27	10	90
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.83	0.77	0.90	347	1129872	48	8	29	11	103
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.92	371	1180013	46	9	23	14	93
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.90	357	1117863	52	9	31	12	96
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.86	0.79	0.92	368	1144943	39	9	21	9	96
CRW_00283	SSU_rRNA_bacteria links to Rfam database...	0.79	0.73	0.84	316	1015651	66	12	46	8	116
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.90	360	1131361	50	9	30	11	96
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	361	1117862	46	11	26	9	97
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.83	0.77	0.90	367	1189245	50	10	31	9	109
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.76	0.70	0.82	322	1123856	83	13	59	11	139
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.53	0.37	0.77	170	1445629	73	4	47	22	292
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.53	0.37	0.77	177	1579523	74	4	49	21	305
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.54	0.37	0.78	185	1611673	73	4	48	21	311
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.45	0.30	0.69	158	2126723	93	6	66	21	376
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.53	0.37	0.76	182	1615264	78	4	53	21	314
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.52	0.36	0.74	177	1665987	83	5	56	22	318
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.93	374	1116361	39	8	22	9	84
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.93	360	1094074	43	2	24	17	85
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.93	364	1119366	44	2	24	18	88
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.88	0.82	0.94	365	1098513	44	3	22	19	81
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.50	0.35	0.72	168	1636913	92	3	61	28	313
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.85	0.77	0.93	344	1215650	51	2	24	25	102
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.80	0.74	0.87	297	945660	69	2	41	26	107
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.90	303	1201687	92	4	31	57	81
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.92	353	1137401	53	5	27	21	94
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.81	0.74	0.88	291	1152590	94	3	37	54	103
CRW_00800	SSU_rRNA_eukarya links to Rfam database...	0.45	0.30	0.67	141	1401765	92	7	62	23	329
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.82	0.76	0.89	358	1117856	57	12	34	11	112
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.93	377	1135871	39	9	21	9	87
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.48	0.33	0.70	167	1606289	89	4	68	17	336
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.52	0.35	0.77	179	1593773	71	4	49	18	327
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.86	0.81	0.92	351	977520	61	3	27	31	83
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.81	0.72	0.92	356	1073456	57	6	27	24	139
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.78	0.66	0.92	354	1500393	66	5	26	35	181
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.75	0.63	0.90	344	1471089	68	3	34	31	203
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.78	0.65	0.92	368	1606129	52	6	25	21	194
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.79	0.68	0.93	367	1433576	53	2	26	25	173
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.80	0.70	0.92	368	1204728	49	8	24	17	159
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.80	0.71	0.90	348	1117874	63	6	32	25	143

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Performance of Fold - scored lower in this pairwise comparison

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP	12415
Total TN	79082106
Total FP	19621
Total FP CONTRA	2495
Total FP INCONS	15311
Total FP COMP	1815
Total FN	17665

Total Scores
MCC	0.412
Average MCC ± 95% Confidence Intervals	0.411 ± 0.027
Sensitivity	0.413
Positive Predictive Value	0.411
Nr of predictions	64

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2. Individual counts for Fold [ 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...	0.56	0.57	0.56	259	1085140	238	22	180	36	199
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.62	0.63	0.61	299	1141829	219	35	153	31	175
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.51	0.51	0.52	239	1170753	241	24	199	18	231
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.40	0.41	0.40	185	1107355	286	30	246	10	271
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.44	0.44	0.44	207	1172278	279	31	230	18	266
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.54	0.54	0.54	259	1181475	236	33	186	17	217
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.43	0.43	0.43	198	1108845	279	32	230	17	259
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.42	0.43	0.42	200	1178403	299	28	249	22	265
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.38	0.38	0.38	176	1135818	299	27	257	15	287
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.53	0.53	0.54	253	1201553	246	34	185	27	223
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.45	0.44	0.45	204	1152472	262	26	219	17	262
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.53	0.52	0.54	246	1179962	231	33	175	23	225
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.40	0.40	0.39	188	1190720	309	32	256	21	280
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.28	0.28	0.28	125	1082214	333	31	286	16	320
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.49	0.48	0.50	226	1178426	251	26	202	23	247
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.45	0.46	0.44	219	1207740	296	42	234	20	256
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.53	0.52	0.54	247	1198465	241	32	182	27	231
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.37	0.37	0.37	167	1105882	297	32	247	18	286
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.49	0.49	0.48	238	1218645	286	36	222	28	246
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.37	0.38	0.37	181	1198432	321	48	265	8	297
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.39	0.39	0.40	183	1192281	294	41	235	18	285
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.54	0.54	0.54	245	1111832	232	27	182	23	210
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.36	0.36	0.37	168	1122293	309	37	253	19	294
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.52	0.52	0.52	233	1085151	238	41	176	21	213
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.59	0.59	0.59	271	1114809	212	28	163	21	186
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.32	0.32	0.32	144	1110348	313	38	265	10	309
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.36	0.35	0.37	159	1129828	293	31	238	24	291
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.58	0.56	0.59	262	1179969	207	27	158	22	202
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.33	0.33	0.32	151	1117794	327	43	272	12	302
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.53	0.52	0.53	243	1144885	238	27	186	25	221
CRW_00283	SSU_rRNA_bacteria links to Rfam database...	0.32	0.32	0.33	140	1015595	312	49	241	22	292
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.29	0.29	0.29	130	1131315	331	40	275	16	326
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.48	0.49	0.48	225	1117789	265	38	208	19	233
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.51	0.50	0.52	237	1189193	251	38	185	28	239
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.41	0.39	0.42	181	1123819	271	41	209	21	280
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.09	0.09	0.08	43	1445337	532	80	390	62	419
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.27	0.29	0.25	138	1579211	437	87	317	33	344
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.34	0.35	0.33	173	1611383	414	61	293	60	323
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.44	0.45	0.44	241	2126401	411	60	251	100	293
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.35	0.36	0.34	177	1614982	392	60	284	48	319
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.29	0.31	0.28	152	1665688	448	68	317	63	343
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.57	0.56	0.57	257	1116315	221	28	165	28	201
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.30	0.30	0.31	133	1094029	317	35	263	19	312
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.42	0.42	0.42	191	1119306	279	34	225	20	261
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.50	0.50	0.50	222	1098458	256	20	203	33	224
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.31	0.32	0.29	156	1636612	443	67	310	66	325
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.20	0.20	0.20	90	1215568	391	45	317	29	356
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.25	0.25	0.25	100	945594	319	37	269	13	304
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.27	0.28	0.26	107	1201617	345	45	256	44	277
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.39	0.38	0.39	172	1137342	303	31	241	31	275
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.32	0.33	0.30	130	1152494	342	43	254	45	264
CRW_00800	SSU_rRNA_eukarya links to Rfam database...	0.52	0.52	0.52	243	1401506	300	34	192	74	227
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.53	0.53	0.52	250	1117779	255	29	202	24	220
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.37	0.38	0.37	175	1135806	315	41	256	18	289
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.36	0.37	0.35	187	1605990	391	60	291	40	316
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.28	0.28	0.27	143	1593476	430	75	311	44	363
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.37	0.36	0.38	158	977486	272	36	221	15	276
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.48	0.46	0.50	229	1073385	256	28	203	25	266
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.46	0.46	0.46	246	1500244	334	36	252	46	289
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.34	0.33	0.34	180	1470946	368	36	308	24	367
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.44	0.44	0.44	245	1605966	343	42	275	26	317
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.46	0.45	0.47	245	1433450	306	32	244	30	295
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.31	0.30	0.33	158	1204643	339	37	290	12	369
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.38	0.38	0.39	186	1117784	320	28	262	30	305

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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(seed) - scored higher in this pairwise comparison

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

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

Performance of Fold - scored lower in this pairwise comparison

1. Total counts & total scores for Fold

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