CompaRNA - on-line benchmarks of RNA structure prediction methods

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Overview

Metric	CentroidAlifold(20)		RNAalifold(seed)
MCC	0.774	>	0.743
Average MCC ± 95% Confidence Intervals	0.769 ± 0.035	>	0.741 ± 0.041
Sensitivity	0.676	<	0.677
Positive Predictive Value	0.886	>	0.817
Total TP	19921	<	19947
Total TN	78832686	>	78830741
Total FP	3948	<	5352
Total FP CONTRA	498	<	1039
Total FP INCONS	2063	<	3441
Total FP COMP	1387	>	872
Total FN	9554	>	9528
P-value	3.56938820447e-08

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Performance plots

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

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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	19921
Total TN	78832686
Total FP	3948
Total FP CONTRA	498
Total FP INCONS	2063
Total FP COMP	1387
Total FN	9554

Total Scores
MCC	0.774
Average MCC ± 95% Confidence Intervals	0.769 ± 0.035
Sensitivity	0.676
Positive Predictive Value	0.886
Nr of predictions	62

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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_00306	SSU_rRNA_eukarya links to Rfam database...	0.52	0.37	0.73	171	1445616	97	6	57	34	291
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.57	0.40	0.80	201	1627859	78	6	44	28	301
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_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_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_00759	SSU_rRNA_eukarya links to Rfam database...	0.51	0.38	0.69	181	1636884	113	8	72	33	300
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
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 RNAalifold(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	19947
Total TN	78830741
Total FP	5352
Total FP CONTRA	1039
Total FP INCONS	3441
Total FP COMP	872
Total FN	9528

Total Scores
MCC	0.743
Average MCC ± 95% Confidence Intervals	0.741 ± 0.041
Sensitivity	0.677
Positive Predictive Value	0.817
Nr of predictions	62

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2. Individual counts for RNAalifold(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...	0.87	0.84	0.90	385	1085175	58	7	34	17	73
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.82	0.77	0.88	363	1141905	62	14	34	14	111
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.88	372	1170793	59	16	34	9	98
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.84	0.81	0.88	369	1107397	60	16	34	10	87
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.82	0.78	0.88	367	1172327	61	16	36	9	106
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.82	0.77	0.88	367	1181535	61	16	35	10	109
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.85	0.81	0.88	370	1108886	58	15	34	9	87
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.89	368	1178465	61	12	35	14	97
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.83	0.79	0.87	367	1135858	62	16	37	9	96
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.88	369	1201606	61	16	34	11	107
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	368	1152515	47	13	25	9	98
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	372	1180006	46	13	25	8	99
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.88	365	1190782	64	12	37	15	103
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.79	0.76	0.84	336	1082254	76	16	50	10	109
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.82	0.77	0.87	364	1178460	66	16	40	10	109
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.82	0.77	0.87	365	1207815	63	16	39	8	110
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.83	0.77	0.88	369	1198508	59	15	34	10	109
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.84	0.81	0.88	366	1105912	60	16	34	10	87
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.82	0.76	0.88	369	1218720	61	16	36	9	115
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.82	0.77	0.88	369	1198505	61	16	36	9	109
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	369	1192333	48	13	25	10	99
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.84	0.81	0.88	368	1111868	59	15	35	9	87
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.90	359	1122350	51	13	29	9	103
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.84	0.80	0.87	358	1085191	60	16	36	8	88
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.84	0.80	0.88	366	1114854	59	16	35	8	91
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.83	0.79	0.87	359	1110382	64	17	37	10	94
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.88	349	1129861	58	13	33	12	101
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.91	372	1180005	54	13	26	15	92
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.84	0.80	0.89	363	1117851	59	13	33	13	90
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.91	372	1144932	48	13	24	11	92
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.89	356	1131358	59	13	33	13	100
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.82	0.78	0.86	356	1117847	66	17	40	9	102
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.80	0.75	0.86	358	1189235	67	16	44	7	118
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.45	0.39	0.52	178	1445508	175	32	132	11	284
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.44	0.37	0.53	184	1627762	174	32	132	10	318
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.44	0.36	0.53	184	1675017	173	32	132	9	323
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.42	0.36	0.51	172	1579413	180	32	136	12	310
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.44	0.36	0.52	181	1611565	175	31	133	11	315
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.44	0.37	0.53	184	1625958	174	32	132	10	314
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.40	0.32	0.50	169	2126616	180	32	136	12	365
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.44	0.35	0.55	182	1750923	164	28	123	13	333
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.45	0.38	0.55	186	1615165	163	28	124	11	310
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.45	0.37	0.54	182	1665890	171	28	125	18	313
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.86	0.82	0.91	377	1116350	49	12	26	11	81
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.86	0.81	0.92	361	1094068	53	6	25	22	84
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.92	366	1119360	52	6	24	22	86
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.92	365	1098507	56	8	23	25	81
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.41	0.34	0.49	163	1636811	183	35	136	12	318
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.81	0.75	0.88	302	945656	72	5	37	30	102
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	355	1137395	59	8	28	23	92
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.78	0.73	0.84	288	1152577	109	10	46	53	106
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.82	0.76	0.88	356	1117856	63	14	34	15	114
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.84	0.80	0.88	372	1135856	59	15	35	9	92
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.41	0.34	0.49	172	1606179	193	36	141	16	331
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.43	0.36	0.52	181	1593657	177	34	133	10	325
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.78	0.69	0.87	344	1073448	73	7	46	20	151
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.74	0.64	0.87	342	1500383	85	10	43	32	193
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.73	0.63	0.86	342	1471073	85	8	47	30	205
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.74	0.63	0.87	355	1606120	72	10	43	19	207
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.76	0.66	0.88	355	1433566	72	7	43	22	185
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.77	0.68	0.87	358	1204715	73	7	48	18	169
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.78	0.70	0.86	346	1117856	80	13	45	22	145

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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 RNAalifold(seed) - scored lower in this pairwise comparison

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

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