CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAalifold(seed)		IPknot
MCC	0.744	>	0.570
Average MCC ± 95% Confidence Intervals	0.742 ± 0.039	>	0.568 ± 0.033
Sensitivity	0.678	>	0.496
Positive Predictive Value	0.818	>	0.656
Total TP	21759	>	15928
Total TN	85766748	<	85769094
Total FP	5870	<	9860
Total FP CONTRA	1107	<	1325
Total FP INCONS	3750	<	7017
Total FP COMP	1013	<	1518
Total FN	10343	<	16174
P-value	3.56938820447e-08

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Performance plots

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

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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	21759
Total TN	85766748
Total FP	5870
Total FP CONTRA	1107
Total FP INCONS	3750
Total FP COMP	1013
Total FN	10343

Total Scores
MCC	0.744
Average MCC ± 95% Confidence Intervals	0.742 ± 0.039
Sensitivity	0.678
Positive Predictive Value	0.818
Nr of predictions	68

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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_00283	SSU_rRNA_bacteria links to Rfam database...	0.80	0.75	0.85	323	1015644	67	14	44	9	109
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_00292	SSU_rRNA_bacteria links to Rfam database...	0.77	0.71	0.84	329	1123856	76	14	51	11	132
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_00763	SSU_rRNA_bacteria links to Rfam database...	0.85	0.78	0.92	348	1215641	59	6	25	28	98
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.81	0.75	0.88	302	945656	72	5	37	30	102
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.86	0.81	0.91	312	1201683	85	4	26	55	72
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_00800	SSU_rRNA_eukarya links to Rfam database...	0.42	0.33	0.52	156	1401675	160	25	119	16	314
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
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.83	0.79	0.88	344	977508	71	5	44	22	90
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 IPknot - scored lower in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	15928
Total TN	85769094
Total FP	9860
Total FP CONTRA	1325
Total FP INCONS	7017
Total FP COMP	1518
Total FN	16174

Total Scores
MCC	0.570
Average MCC ± 95% Confidence Intervals	0.568 ± 0.033
Sensitivity	0.496
Positive Predictive Value	0.656
Nr of predictions	68

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2. Individual counts for IPknot [ 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...	0.83	0.77	0.89	352	1085204	78	4	41	33	106
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.78	0.76	0.79	360	1141862	121	19	75	27	114
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.72	0.63	0.83	297	1170856	75	6	56	13	173
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.58	0.50	0.66	229	1107469	137	16	102	19	227
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.71	0.61	0.83	287	1172399	74	4	56	14	186
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.66	0.60	0.72	287	1181556	121	23	87	11	189
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.59	0.52	0.66	236	1108950	134	23	96	15	221
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.55	0.50	0.60	231	1178495	170	17	137	16	234
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.76	0.68	0.83	317	1135898	79	6	57	16	146
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.70	0.64	0.77	307	1201626	111	11	81	19	169
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.58	0.50	0.68	231	1152582	123	17	91	15	235
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.54	0.48	0.62	225	1180051	148	20	120	8	246
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.61	0.53	0.70	249	1190838	118	6	103	9	219
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.37	0.34	0.40	150	1082284	231	30	192	9	295
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.59	0.53	0.65	252	1178495	145	17	116	12	221
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.61	0.55	0.67	261	1207844	146	17	113	16	214
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.73	0.63	0.85	302	1198569	73	7	48	18	176
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.62	0.53	0.74	239	1106005	96	13	71	12	214
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.76	0.72	0.81	347	1218713	108	15	66	27	137
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.57	0.52	0.63	250	1198526	164	23	127	14	228
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.56	0.44	0.71	207	1192448	104	18	67	19	261
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.66	0.55	0.79	250	1111971	79	11	54	14	205
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.56	0.47	0.66	216	1122424	126	25	86	15	246
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.52	0.47	0.58	208	1085244	163	20	129	14	238
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.76	0.69	0.83	314	1114894	79	11	52	16	143
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.53	0.43	0.66	194	1110503	106	22	76	8	259
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.60	0.48	0.74	218	1129962	95	5	71	19	232
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.66	0.58	0.76	270	1180060	100	16	70	14	194
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.67	0.58	0.77	265	1117916	90	11	68	11	188
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.65	0.59	0.72	276	1144958	123	17	90	16	188
CRW_00283	SSU_rRNA_bacteria links to Rfam database...	0.42	0.31	0.56	136	1015781	124	17	91	16	296
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.55	0.42	0.71	193	1131487	92	13	67	12	263
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.79	0.71	0.88	327	1117890	60	13	30	17	131
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.64	0.56	0.73	268	1189284	121	17	84	20	208
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.41	0.35	0.48	160	1123920	187	28	142	17	301
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.28	0.24	0.34	109	1445531	252	37	173	42	353
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.53	0.43	0.66	216	1627783	139	27	84	28	286
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.39	0.34	0.43	174	1674963	268	35	193	40	333
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.37	0.32	0.42	153	1579390	248	42	168	38	329
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.49	0.41	0.59	203	1611565	179	27	115	37	293
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.45	0.41	0.50	202	1625901	232	30	173	29	296
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.49	0.40	0.59	214	2126590	218	30	119	69	320
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.29	0.27	0.32	141	1750812	337	58	245	34	374
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.40	0.34	0.46	170	1615137	238	31	165	42	326
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.41	0.33	0.51	163	1665906	188	30	126	32	332
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.81	0.75	0.88	344	1116375	69	10	36	23	114
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.44	0.37	0.53	164	1094152	163	21	123	19	281
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.53	0.48	0.59	217	1119386	165	27	126	12	235
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.70	0.63	0.77	282	1098536	110	15	70	25	164
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.28	0.24	0.33	116	1636796	279	54	179	46	365
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.48	0.34	0.67	153	1215790	109	10	67	32	293
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.44	0.34	0.57	136	945760	126	16	88	22	268
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.42	0.29	0.60	111	1201840	104	12	62	30	273
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.55	0.46	0.66	206	1137473	121	11	96	14	241
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.36	0.26	0.50	102	1152715	143	20	84	39	292
CRW_00800	SSU_rRNA_eukarya links to Rfam database...	0.62	0.51	0.75	240	1401657	117	12	66	39	230
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.68	0.63	0.73	295	1117857	132	9	99	24	175
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.68	0.62	0.75	289	1135893	113	17	79	17	175
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.37	0.35	0.40	174	1606096	291	43	215	33	329
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.45	0.41	0.50	207	1593595	240	34	169	37	299
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.50	0.42	0.59	182	977595	134	16	108	10	252
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.64	0.57	0.72	282	1073454	132	13	96	23	213
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.67	0.62	0.73	331	1500326	158	17	104	37	204
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.55	0.46	0.66	252	1471087	150	21	110	19	295
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.62	0.57	0.67	319	1606055	171	20	134	17	243
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.69	0.63	0.76	342	1433519	132	10	100	22	198
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.56	0.48	0.66	252	1204748	138	22	106	10	275
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.61	0.56	0.67	276	1117847	163	10	127	26	215

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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 IPknot - scored lower in this pairwise comparison

1. Total counts & total scores for IPknot

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