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(seed)		Carnac(20)
MCC	0.799	>	0.597
Average MCC ± 95% Confidence Intervals	0.793 ± 0.033	>	0.593 ± 0.021
Sensitivity	0.708	>	0.390
Positive Predictive Value	0.901	<	0.914
Total TP	19446	>	10699
Total TN	72152542	<	72162430
Total FP	3058	>	1637
Total FP CONTRA	409	>	140
Total FP INCONS	1734	>	862
Total FP COMP	915	>	635
Total FN	8007	<	16754
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of CentroidAlifold(seed) and Carnac(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 Carnac(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 Carnac(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(seed) and Carnac(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 Carnac(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 Carnac(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	10699
Total TN	72162430
Total FP	1637
Total FP CONTRA	140
Total FP INCONS	862
Total FP COMP	635
Total FN	16754

Total Scores
MCC	0.597
Average MCC ± 95% Confidence Intervals	0.593 ± 0.021
Sensitivity	0.390
Positive Predictive Value	0.914
Nr of predictions	58

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2. Individual counts for Carnac(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...	0.74	0.59	0.94	270	1085313	35	5	13	17	188
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.56	0.35	0.90	166	1142131	28	4	15	9	308
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.62	0.43	0.91	202	1170992	29	3	18	8	268
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.62	0.42	0.91	191	1107607	23	4	14	5	265
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.64	0.43	0.95	204	1172532	17	3	7	7	269
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.63	0.42	0.94	199	1181742	19	2	10	7	277
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.69	0.51	0.94	234	1109056	28	2	13	13	223
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.62	0.43	0.92	198	1178664	29	0	18	11	267
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.71	0.53	0.95	246	1136018	21	2	12	7	217
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.64	0.43	0.93	207	1201802	26	4	12	10	269
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.66	0.46	0.95	216	1152694	16	3	8	5	250
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.69	0.52	0.92	244	1180151	26	4	17	5	227
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.64	0.44	0.93	207	1190974	24	0	15	9	261
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.56	0.36	0.89	158	1082478	26	2	18	6	287
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.52	0.32	0.87	149	1178708	29	3	20	6	324
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.64	0.43	0.96	204	1208022	12	2	7	3	271
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.66	0.47	0.93	227	1198681	28	3	15	10	251
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.65	0.45	0.93	205	1106108	20	3	12	5	248
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.56	0.35	0.91	168	1218956	27	4	13	10	316
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.68	0.50	0.91	241	1198660	33	4	21	8	237
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.64	0.43	0.97	200	1192533	11	3	4	4	268
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.66	0.47	0.93	212	1112057	22	4	13	5	243
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.62	0.41	0.94	191	1122548	17	3	9	5	271
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.57	0.35	0.92	156	1085431	16	4	10	2	290
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.60	0.37	0.95	171	1115091	13	2	7	4	286
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.64	0.44	0.93	201	1110578	20	3	13	4	252
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.52	0.29	0.92	130	1130115	15	4	7	4	320
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.68	0.51	0.92	237	1180158	31	3	18	10	227
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.66	0.46	0.96	209	1118042	12	1	8	3	244
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.65	0.45	0.95	209	1145120	17	2	10	5	255
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.53	0.33	0.87	150	1131587	27	3	20	4	306
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.62	0.41	0.93	188	1118058	18	2	12	4	270
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.58	0.41	0.84	194	1189422	41	5	32	4	282
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.55	0.32	0.95	146	1445697	38	0	7	31	316
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.47	0.25	0.87	122	1579613	37	1	17	19	360
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.48	0.29	0.81	143	1611733	59	1	33	25	353
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.49	0.26	0.93	140	2126802	50	1	10	39	394
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.39	0.19	0.81	94	1615387	42	0	22	20	402
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.38	0.19	0.74	96	1666095	60	1	33	26	399
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.62	0.42	0.91	192	1116554	28	4	15	9	266
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.58	0.35	0.97	156	1094299	10	0	5	5	289
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.55	0.33	0.93	148	1119597	15	1	10	4	304
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.66	0.46	0.93	206	1098682	26	1	14	11	240
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.39	0.19	0.79	93	1637028	51	3	21	27	388
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.48	0.30	0.77	122	945842	42	3	33	6	282
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.61	0.43	0.88	191	1137570	34	1	24	9	256
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.59	0.38	0.90	150	1152755	40	0	16	24	244
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.62	0.42	0.92	196	1118046	27	3	15	9	274
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.60	0.39	0.93	181	1136084	19	3	10	6	283
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.44	0.25	0.76	126	1606363	56	1	38	17	377
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.47	0.25	0.90	125	1593866	44	0	14	30	381
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.60	0.40	0.92	196	1073633	28	3	13	12	299
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.62	0.41	0.95	218	1500548	29	3	9	17	317
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.59	0.38	0.92	206	1471246	35	2	16	17	341
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.62	0.40	0.96	226	1606292	20	3	7	10	336
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.58	0.36	0.94	192	1433767	24	1	11	12	348
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.62	0.41	0.93	216	1204895	30	4	13	13	311
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.66	0.48	0.92	234	1118007	37	4	15	18	257

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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 Carnac(20) - scored lower in this pairwise comparison

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

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