CompaRNA - on-line benchmarks of RNA structure prediction methods

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Overview

Metric	RNAalifold(seed)		MXScarna(20)
MCC	0.743	>	0.637
Average MCC ± 95% Confidence Intervals	0.741 ± 0.041	>	0.641 ± 0.028
Sensitivity	0.677	>	0.581
Positive Predictive Value	0.817	>	0.699
Total TP	19947	>	17132
Total TN	78830741	>	78830642
Total FP	5352	<	10102
Total FP CONTRA	1039	<	1141
Total FP INCONS	3441	<	6253
Total FP COMP	872	<	2708
Total FN	9528	<	12343
P-value	3.56938820447e-08

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Performance plots

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

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Performance of RNAalifold(seed) - scored higher 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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Performance of MXScarna(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	17132
Total TN	78830642
Total FP	10102
Total FP CONTRA	1141
Total FP INCONS	6253
Total FP COMP	2708
Total FN	12343

Total Scores
MCC	0.637
Average MCC ± 95% Confidence Intervals	0.641 ± 0.028
Sensitivity	0.581
Positive Predictive Value	0.699
Nr of predictions	62

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2. Individual counts for MXScarna(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...	0.84	0.81	0.87	369	1085176	107	10	46	51	89
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.68	0.60	0.77	283	1141947	122	12	74	36	191
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.72	0.67	0.78	317	1170807	127	11	80	36	153
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.68	0.63	0.74	288	1107425	137	16	87	34	168
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.72	0.66	0.78	312	1172344	127	16	74	37	161
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.73	0.66	0.81	316	1181563	109	13	61	35	160
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.69	0.64	0.74	293	1108909	137	18	85	34	164
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.75	0.68	0.81	318	1178489	108	6	67	35	147
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.76	0.71	0.81	328	1135874	114	12	64	38	135
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.69	0.64	0.75	305	1201619	132	14	87	31	171
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.72	0.65	0.80	303	1152540	113	14	64	35	163
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.76	0.70	0.82	332	1180009	110	11	64	35	139
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.65	0.60	0.71	281	1190800	160	10	105	45	187
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.57	0.52	0.63	232	1082285	168	19	120	29	213
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.62	0.56	0.68	264	1178492	152	16	108	28	209
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.73	0.67	0.80	319	1207837	117	10	69	38	156
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.73	0.67	0.80	319	1198526	122	12	69	41	159
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.73	0.67	0.81	302	1105955	106	13	58	35	151
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.71	0.65	0.77	317	1218729	129	13	82	34	167
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.73	0.67	0.79	321	1198521	119	12	72	35	157
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.70	0.64	0.77	299	1192353	124	11	77	36	169
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.72	0.67	0.77	306	1111891	121	14	75	32	149
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.70	0.65	0.77	298	1122364	122	17	72	33	164
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.68	0.62	0.74	277	1085225	135	13	86	36	169
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.71	0.63	0.80	289	1114908	114	13	61	40	168
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.68	0.63	0.73	286	1110405	132	17	87	28	167
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.71	0.62	0.80	280	1129906	107	12	58	37	170
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.70	0.64	0.77	299	1180027	133	10	80	43	165
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.72	0.66	0.78	301	1117875	125	10	74	41	152
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.71	0.65	0.78	303	1144954	117	13	71	33	161
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.69	0.62	0.77	281	1131397	117	9	73	35	175
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.70	0.64	0.77	292	1117883	123	15	70	38	166
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.62	0.58	0.66	274	1189239	172	18	122	32	202
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.43	0.40	0.46	183	1445453	276	47	167	62	279
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.49	0.45	0.53	227	1627679	267	35	169	63	275
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.48	0.44	0.53	224	1674941	262	38	162	62	283
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.42	0.40	0.43	195	1579299	332	47	212	73	287
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.49	0.46	0.53	229	1611474	266	39	168	59	267
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.51	0.47	0.54	236	1625872	273	37	161	75	262
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.37	0.33	0.42	175	2126532	323	40	206	77	359
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.47	0.43	0.50	223	1750812	281	44	177	60	292
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.49	0.46	0.52	227	1615066	271	42	168	61	269
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.39	0.37	0.41	181	1665782	316	50	212	54	314
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.63	0.58	0.69	266	1116382	147	16	101	30	192
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.69	0.62	0.76	277	1094097	130	6	80	44	168
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.72	0.67	0.78	303	1119366	134	11	76	47	149
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.74	0.68	0.81	303	1098531	115	7	62	46	143
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.42	0.40	0.44	191	1636712	314	43	199	72	290
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.60	0.54	0.67	217	945677	148	10	96	42	187
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.67	0.60	0.75	268	1137427	134	8	83	43	179
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.63	0.57	0.71	224	1152605	176	10	82	84	170
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.61	0.55	0.68	260	1117878	154	17	105	32	210
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.74	0.69	0.79	322	1135872	121	12	72	37	142
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.44	0.42	0.46	211	1606072	295	46	199	50	292
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.48	0.45	0.51	229	1593556	274	47	173	54	277
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.69	0.60	0.79	295	1073472	114	10	68	36	200
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.62	0.51	0.75	274	1500415	142	2	87	53	261
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.66	0.56	0.78	308	1471077	135	7	78	50	239
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.61	0.52	0.71	293	1606118	156	16	101	39	269
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.64	0.54	0.75	291	1433583	134	3	94	37	249
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.66	0.57	0.76	302	1204732	134	11	83	40	225
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.69	0.60	0.79	294	1117886	120	10	70	40	197

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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 RNAalifold(seed) - scored higher in this pairwise comparison

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

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

Performance of MXScarna(20) - scored lower in this pairwise comparison

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

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