CompaRNA - on-line benchmarks of RNA structure prediction methods

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Overview

Metric	CentroidAlifold(seed)		RSpredict(20)
MCC	0.799	>	0.591
Average MCC ± 95% Confidence Intervals	0.793 ± 0.033	>	0.594 ± 0.057
Sensitivity	0.708	>	0.530
Positive Predictive Value	0.901	>	0.659
Total TP	19446	>	14560
Total TN	72152542	>	72152050
Total FP	3058	<	9115
Total FP CONTRA	409	<	1285
Total FP INCONS	1734	<	6236
Total FP COMP	915	<	1594
Total FN	8007	<	12893
P-value	3.56938820447e-08

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Performance plots

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

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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	19446
Total TN	72152542
Total FP	3058
Total FP CONTRA	409
Total FP INCONS	1734
Total FP COMP	915
Total FN	8007

Total Scores
MCC	0.799
Average MCC ± 95% Confidence Intervals	0.793 ± 0.033
Sensitivity	0.708
Positive Predictive Value	0.901
Nr of predictions	58

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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_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_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_00772	SSU_rRNA_bacteria links to Rfam database...	0.80	0.74	0.87	297	945660	69	2	41	26	107
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_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
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 RSpredict(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	14560
Total TN	72152050
Total FP	9115
Total FP CONTRA	1285
Total FP INCONS	6236
Total FP COMP	1594
Total FN	12893

Total Scores
MCC	0.591
Average MCC ± 95% Confidence Intervals	0.594 ± 0.057
Sensitivity	0.530
Positive Predictive Value	0.659
Nr of predictions	58

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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_00306	SSU_rRNA_eukarya links to Rfam database...	0.37	0.34	0.39	158	1445446	293	34	212	47	304
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.01	0.01	0.01	4	1579393	371	66	290	15	478
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1611495	424	63	344	17	488
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	2126541	465	66	346	53	534
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_00759	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	9	1636732	429	64	340	25	472
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
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 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 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 ]