CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ContextFold		PknotsRG
MCC	0.741	>	0.363
Average MCC ± 95% Confidence Intervals	0.711 ± 0.032	>	0.364 ± 0.022
Sensitivity	0.696	>	0.363
Positive Predictive Value	0.789	>	0.363
Total TP	38384	>	19991
Total TN	137613803	>	137607460
Total FP	16120	<	42527
Total FP CONTRA	2078	<	5822
Total FP INCONS	8198	<	29190
Total FP COMP	5844	<	7515
Total FN	16748	<	35141
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of ContextFold and PknotsRG. 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 ContextFold and PknotsRG).
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 ContextFold and PknotsRG).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and PknotsRG. 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 ContextFold and PknotsRG).

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Performance of ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP	38384
Total TN	137613803
Total FP	16120
Total FP CONTRA	2078
Total FP INCONS	8198
Total FP COMP	5844
Total FN	16748

Total Scores
MCC	0.741
Average MCC ± 95% Confidence Intervals	0.711 ± 0.032
Sensitivity	0.696
Positive Predictive Value	0.789
Nr of predictions	168

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00002	-	0.59	0.52	0.69	136	408862	102	9	53	40	128
CRW_00024	SSU_rRNA_archaea links to Rfam database...	0.95	0.92	0.98	423	1085170	15	3	5	7	35
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.91	0.89	0.93	421	1141864	43	16	15	12	53
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.94	0.90	0.98	421	1170787	8	3	4	1	49
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.94	0.90	0.97	412	1107393	12	2	9	1	44
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.91	0.88	0.95	416	1172309	22	2	19	1	57
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.94	0.90	0.97	429	1181511	14	7	6	1	47
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.95	0.92	0.99	421	1108878	11	2	4	5	36
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.96	0.92	0.99	430	1178445	8	0	5	3	35
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.93	0.90	0.97	415	1135850	16	2	11	3	48
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.93	0.89	0.97	426	1201584	22	4	11	7	50
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.85	0.81	0.90	376	1152502	48	6	37	5	90
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.91	0.87	0.95	412	1179984	23	8	12	3	59
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.95	0.91	0.99	427	1190763	11	0	6	5	41
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.78	0.71	0.85	318	1082280	60	6	52	2	127
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.92	0.88	0.97	417	1178448	25	2	13	10	56
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.94	0.89	1.00	424	1207810	4	1	0	3	51
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.94	0.90	0.97	431	1198483	18	4	8	6	47
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.93	0.89	0.97	404	1105911	13	2	11	0	49
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.92	0.89	0.96	433	1218688	25	3	17	5	51
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.94	0.91	0.98	435	1198481	12	4	6	2	43
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.91	376	1192327	51	4	33	14	92
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.91	0.86	0.95	391	1111876	31	0	19	12	64
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.92	0.88	0.98	405	1122336	12	2	8	2	57
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.91	0.86	0.97	383	1085207	14	1	10	3	63
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.94	0.90	0.98	412	1114849	15	3	7	5	45
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.83	0.79	0.87	359	1110384	57	9	43	5	94
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.77	0.70	0.84	316	1129880	68	9	51	8	134
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.89	0.84	0.94	389	1180004	36	4	19	13	75
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.92	0.88	0.95	398	1117843	21	4	15	2	55
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.92	0.87	0.96	405	1144919	21	2	15	4	59
CRW_00283	SSU_rRNA_bacteria links to Rfam database...	0.75	0.69	0.81	298	1015659	88	12	56	20	134
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.89	365	1131352	48	0	43	5	91
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.95	0.91	0.99	416	1117839	7	2	3	2	42
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.90	382	1189229	44	4	38	2	94
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.76	0.70	0.81	325	1123851	81	12	62	7	136
CRW_00338	-	0.25	0.26	0.25	102	1053015	324	55	254	15	293
CRW_00381	-	0.56	0.54	0.59	299	2303227	281	32	173	76	258
CRW_00417	-	0.87	0.80	0.95	209	458183	19	2	9	8	53
CRW_00418	-	0.66	0.58	0.75	152	441127	54	6	45	3	108
CRW_00419	-	0.78	0.70	0.88	186	463954	32	6	20	6	79
CRW_00421	-	0.77	0.71	0.84	188	462978	47	6	31	10	78
CRW_00422	-	0.90	0.81	0.99	214	455318	14	0	3	11	49
CRW_00424	-	0.69	0.63	0.77	228	789098	94	11	59	24	135
CRW_00426	-	0.88	0.81	0.97	214	457225	18	0	7	11	51
CRW_00427	-	0.80	0.74	0.88	192	454363	31	5	21	5	69
CRW_00428	-	0.80	0.71	0.89	185	465888	28	2	20	6	75
CRW_00430	-	0.76	0.71	0.83	188	456263	46	7	32	7	78
CRW_00433	-	0.83	0.73	0.94	192	467823	17	2	11	4	71
CRW_00434	-	0.87	0.77	0.97	203	457237	12	3	3	6	60
CRW_00435	-	0.60	0.51	0.69	136	451528	71	6	55	10	129
CRW_00437	-	0.85	0.77	0.94	199	456279	19	1	11	7	61
CRW_00438	-	0.75	0.66	0.84	178	454369	43	5	29	9	90
CRW_00441	-	0.84	0.76	0.93	198	454368	21	1	14	6	64
CRW_00442	-	0.76	0.68	0.84	178	453416	46	4	30	12	83
CRW_00443	-	0.61	0.53	0.70	138	456292	71	7	53	11	122
CRW_00444	-	0.89	0.81	0.98	214	459143	13	2	2	9	49
CRW_00445	-	0.86	0.76	0.97	202	458195	11	1	5	5	63
CRW_00446	-	0.86	0.79	0.93	209	468771	29	3	13	13	56
CRW_00447	-	0.61	0.58	0.66	150	452447	84	15	64	5	110
CRW_00448	-	0.86	0.76	0.97	198	457241	20	1	6	13	63
CRW_00449	-	0.83	0.76	0.91	197	444879	26	7	13	6	63
CRW_00450	-	0.76	0.68	0.84	178	458191	47	6	28	13	84
CRW_00451	-	0.84	0.76	0.92	201	457228	26	4	13	9	63
CRW_00452	-	0.88	0.79	0.98	208	453415	14	3	2	9	54
CRW_00453	-	0.75	0.66	0.86	172	452477	34	3	24	7	89
CRW_00456	-	0.82	0.74	0.91	195	470720	26	2	18	6	70
CRW_00457	-	0.86	0.78	0.95	207	467811	23	3	7	13	57
CRW_00458	-	0.91	0.84	0.98	223	464902	16	2	3	11	41
CRW_00459	-	0.87	0.79	0.96	207	462025	19	0	9	10	56
CRW_00462	-	0.79	0.70	0.88	183	458196	30	6	18	6	78
CRW_00463	-	0.75	0.69	0.82	176	445825	42	11	28	3	78
CRW_00464	-	0.88	0.80	0.97	212	462022	14	2	5	7	52
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.95	0.92	0.98	421	1116336	10	3	5	2	37
CRW_00522	-	0.31	0.28	0.33	221	3642980	461	77	372	12	561
CRW_00530	-	0.29	0.28	0.30	74	534851	176	43	127	6	194
CRW_00532	-	0.15	0.14	0.15	38	579171	226	55	162	9	227
CRW_00533	-	0.54	0.53	0.56	115	453422	146	34	57	55	104
CRW_00535	-	0.45	0.44	0.47	144	898162	183	38	126	19	184
CRW_00538	-	0.31	0.29	0.34	88	811913	189	31	143	15	212
CRW_00542	-	0.20	0.21	0.20	67	994418	300	70	200	30	250
CRW_00545	-	0.20	0.21	0.19	41	1343766	290	65	108	117	152
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.90	350	1094071	49	3	36	10	95
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	358	1119364	45	3	31	11	94
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.92	0.88	0.96	393	1098492	32	6	12	14	53
CRW_00594	-	0.21	0.21	0.21	83	1028491	337	39	282	16	312
CRW_00596	-	0.53	0.51	0.55	198	1024237	183	25	136	22	188
CRW_00597	-	0.36	0.35	0.38	143	1200100	258	38	194	26	268
CRW_00604	-	0.76	0.77	0.76	62	411696	170	7	13	150	19
CRW_00606	-	0.55	0.57	0.54	52	559057	214	15	29	170	40
CRW_00607	-	0.82	0.77	0.88	59	536063	209	0	8	201	18
CRW_00615	-	0.73	0.71	0.75	58	553801	230	14	5	211	24
CRW_00617	-	0.35	0.38	0.32	24	426351	179	22	29	128	40
CRW_00678	-	0.48	0.51	0.45	62	666296	245	14	63	168	59
CRW_00680	-	0.88	0.84	0.92	102	516525	157	3	6	148	20
CRW_00683	-	0.61	0.64	0.58	86	460172	167	26	36	105	49
CRW_00684	-	0.60	0.64	0.56	86	612017	209	26	42	141	49
CRW_00702	-	0.74	0.79	0.69	59	357350	156	19	7	130	16
CRW_00704	-	0.58	0.54	0.61	51	386677	165	11	21	133	43
CRW_00706	-	0.54	0.63	0.47	37	695531	262	23	19	220	22
CRW_00710	-	0.65	0.63	0.68	72	1040297	294	10	24	260	42
CRW_00712	-	0.59	0.58	0.61	63	952786	270	6	35	229	45
CRW_00713	-	0.64	0.59	0.70	60	731359	250	4	22	224	41
CRW_00730	-	0.56	0.57	0.55	92	338909	135	20	55	60	69
CRW_00734	-	0.28	0.32	0.25	35	537028	200	40	63	97	75
CRW_00735	-	0.29	0.36	0.23	43	677847	241	75	65	101	78
CRW_00740	-	0.18	0.19	0.17	21	489430	212	17	87	108	92
CRW_00745	-	0.49	0.51	0.47	79	1343812	314	19	70	225	75
CRW_00746	-	0.50	0.51	0.49	111	550500	161	34	80	47	108
CRW_00750	-	0.57	0.56	0.57	90	709679	189	15	52	122	70
CRW_00751	-	0.48	0.49	0.47	87	489370	165	33	65	67	91
CRW_00753	-	0.09	0.10	0.09	17	489362	239	44	132	63	161
CRW_00757	-	0.08	0.09	0.07	11	415255	219	48	102	69	115
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.75	0.69	0.82	306	1215649	111	12	53	46	140
CRW_00765	-	0.86	0.79	0.93	203	452457	30	4	12	14	54
CRW_00766	-	0.41	0.38	0.45	92	440185	127	14	100	13	148
CRW_00768	-	0.83	0.76	0.92	196	471692	35	1	17	17	63
CRW_00769	-	0.69	0.62	0.78	155	451525	53	9	36	8	97
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.71	0.65	0.79	262	945667	95	9	62	24	142
CRW_00773	-	0.80	0.74	0.87	192	451505	40	1	27	12	67
CRW_00774	-	0.85	0.78	0.94	205	488347	28	1	13	14	58
CRW_00777	-	0.46	0.44	0.48	135	719120	172	28	117	27	169
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.71	0.64	0.79	246	1201714	124	13	52	59	138
CRW_00779	-	0.48	0.44	0.53	184	1031419	181	18	145	18	238
CRW_00780	-	0.81	0.73	0.90	185	475594	40	5	16	19	70
CRW_00783	-	0.82	0.73	0.93	188	453425	24	2	13	9	71
CRW_00784	-	0.88	0.80	0.96	210	456272	24	2	6	16	52
CRW_00785	-	0.80	0.72	0.88	183	452468	37	3	22	12	70
CRW_00787	-	0.47	0.44	0.50	134	646683	154	23	113	18	172
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.91	357	1137392	54	3	34	17	90
CRW_00793	-	0.54	0.50	0.58	189	1048748	192	25	114	53	188
CRW_00794	-	0.57	0.50	0.64	123	434586	76	10	59	7	123
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.65	0.59	0.71	232	1152596	140	14	79	47	162
CRW_00796	-	0.47	0.41	0.55	96	384827	87	6	74	7	139
CRW_00797	-	0.41	0.39	0.44	132	692956	181	21	144	16	210
CRW_00800	SSU_rRNA_eukarya links to Rfam database...	0.83	0.77	0.89	361	1401569	111	5	40	66	109
CRW_00801	-	0.72	0.68	0.76	169	438295	67	11	41	15	80
CRW_00802	-	0.69	0.64	0.75	162	460104	68	15	39	14	91
CRW_00807	-	0.59	0.56	0.62	224	1391587	214	15	120	79	174
CRW_00808	-	0.35	0.33	0.38	117	1301385	278	50	139	89	239
CRW_00813	-	0.36	0.39	0.33	52	530805	210	44	64	102	81
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.93	0.90	0.96	425	1117816	31	1	18	12	45
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.92	0.90	0.95	419	1135835	28	6	18	4	45
CRW_01134	-	0.68	0.63	0.75	267	964999	103	10	79	14	160
CRW_01168	-	0.79	0.73	0.86	298	900806	67	5	44	18	113
CRW_01186	-	0.81	0.76	0.87	293	836234	52	8	36	8	93
CRW_01188	-	0.50	0.46	0.54	180	837529	163	17	139	7	213
CRW_01189	-	0.58	0.54	0.63	211	862304	132	17	109	6	181
CRW_01214	-	0.79	0.73	0.87	295	931954	52	12	34	6	110
CRW_01222	-	0.59	0.54	0.66	213	912953	120	18	92	10	184
CRW_01224	-	0.76	0.70	0.83	276	912945	62	8	47	7	121
CRW_01239	-	0.56	0.51	0.61	193	840140	134	22	101	11	189
CRW_01250	-	0.79	0.71	0.88	269	781568	41	5	33	3	109
CRW_01260	-	0.73	0.64	0.82	252	912969	76	0	55	21	141
CRW_01266	-	0.78	0.73	0.84	278	818229	67	5	48	14	103
CRW_01271	-	0.58	0.54	0.63	205	827215	135	18	103	14	176
CRW_01275	-	0.79	0.74	0.84	321	1082273	75	15	47	13	111
CRW_01283	-	0.80	0.73	0.87	299	963624	64	6	37	21	110
CRW_01314	-	0.69	0.61	0.78	249	937446	74	11	59	4	158
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.82	0.76	0.89	328	977531	59	6	36	17	106
CRW_01344	-	0.67	0.62	0.73	226	791602	94	9	74	11	140
PDB_00409	-	0.60	0.61	0.60	149	688301	225	27	74	124	96
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.87	0.79	0.96	392	1073435	37	4	14	19	103
PDB_00805	-	0.65	0.61	0.69	183	467763	101	10	72	19	119
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.90	0.85	0.96	459	1433493	36	3	16	17	81
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.88	0.80	0.97	422	1204693	33	2	11	20	105
PDB_01261	-	0.68	0.58	0.79	196	467781	51	4	47	0	140
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.86	0.78	0.94	385	1117852	50	4	19	27	106

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Performance of PknotsRG - scored lower in this pairwise comparison

1. Total counts & total scores for PknotsRG

Total Base Pair Counts
Total TP	19991
Total TN	137607460
Total FP	42527
Total FP CONTRA	5822
Total FP INCONS	29190
Total FP COMP	7515
Total FN	35141

Total Scores
MCC	0.363
Average MCC ± 95% Confidence Intervals	0.364 ± 0.022
Sensitivity	0.363
Positive Predictive Value	0.363
Nr of predictions	168

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00002	-	0.59	0.56	0.62	147	408824	142	7	82	53	117
CRW_00024	SSU_rRNA_archaea links to Rfam database...	0.77	0.76	0.79	348	1085160	130	18	75	37	110
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.63	0.63	0.63	300	1141843	196	31	142	23	174
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.45	0.45	0.45	210	1170748	276	27	230	19	260
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.53	0.52	0.54	236	1107378	216	34	168	14	220
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.50	0.49	0.51	233	1172293	234	28	192	14	240
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.43	0.44	0.43	208	1181469	284	32	244	8	268
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.33	0.33	0.34	152	1108852	312	37	264	11	305
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.55	0.55	0.55	255	1178420	227	21	184	22	210
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.64	0.64	0.65	296	1135820	182	22	140	20	167
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.51	0.50	0.52	238	1201566	240	29	192	19	238
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.41	0.41	0.42	190	1152467	282	34	230	18	276
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.51	0.50	0.52	236	1179961	240	37	182	21	235
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.53	0.52	0.54	242	1190746	234	25	183	26	226
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.29	0.29	0.29	128	1082212	325	37	279	9	317
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.42	0.41	0.42	196	1178413	284	31	240	13	277
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.47	0.46	0.47	220	1207767	270	26	222	22	255
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.55	0.54	0.57	260	1198467	221	30	169	22	218
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.35	0.35	0.34	157	1105872	312	45	254	13	296
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.57	0.57	0.58	275	1218668	230	24	174	32	209
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.43	0.43	0.43	205	1198449	287	30	242	15	273
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.45	0.44	0.46	206	1192291	257	41	202	14	262
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.38	0.37	0.39	168	1111857	279	39	222	18	287
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.49	0.48	0.50	220	1122307	239	36	188	15	242
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.51	0.50	0.51	222	1085169	227	31	179	17	224
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.42	0.42	0.43	193	1114817	278	26	235	17	264
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.25	0.25	0.24	113	1110332	354	55	295	4	340
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.41	0.40	0.42	180	1129825	270	35	216	19	270
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.29	0.29	0.30	134	1179968	334	40	274	20	330
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.50	0.50	0.51	226	1117813	234	28	193	13	227
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.30	0.30	0.30	138	1144878	340	40	285	15	326
CRW_00283	SSU_rRNA_bacteria links to Rfam database...	0.28	0.28	0.29	120	1015605	317	42	258	17	312
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.26	0.25	0.26	115	1131320	336	35	290	11	341
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.47	0.47	0.47	214	1117807	257	31	208	18	244
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.45	0.44	0.46	209	1189197	272	34	213	25	267
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.31	0.30	0.32	138	1123818	305	44	250	11	323
CRW_00338	-	0.15	0.16	0.14	64	1052952	418	71	339	8	331
CRW_00381	-	0.33	0.34	0.32	189	2303139	503	71	332	100	368
CRW_00417	-	0.38	0.37	0.39	97	458154	163	22	130	11	165
CRW_00418	-	0.17	0.16	0.19	42	441104	195	25	159	11	218
CRW_00419	-	0.26	0.25	0.28	66	463932	175	16	152	7	199
CRW_00421	-	0.34	0.32	0.36	86	462964	166	22	131	13	180
CRW_00422	-	0.38	0.37	0.39	97	455287	169	22	129	18	166
CRW_00424	-	0.38	0.39	0.38	140	789031	253	23	202	28	223
CRW_00426	-	0.26	0.25	0.27	66	457200	190	24	156	10	199
CRW_00427	-	0.24	0.23	0.25	61	454339	196	32	149	15	200
CRW_00428	-	0.29	0.28	0.30	73	465855	179	27	140	12	187
CRW_00430	-	0.33	0.31	0.36	82	456260	154	27	121	6	184
CRW_00433	-	0.37	0.34	0.40	89	467805	139	16	118	5	174
CRW_00434	-	0.24	0.22	0.26	59	457218	179	11	158	10	204
CRW_00435	-	0.33	0.31	0.36	81	451499	155	16	129	10	184
CRW_00437	-	0.21	0.21	0.22	54	456243	200	25	168	7	206
CRW_00438	-	0.35	0.34	0.36	91	454325	175	25	140	10	177
CRW_00441	-	0.17	0.16	0.19	42	454358	185	31	150	4	220
CRW_00442	-	0.38	0.36	0.39	94	453389	153	25	120	8	167
CRW_00443	-	0.40	0.37	0.43	96	456268	147	23	103	21	164
CRW_00444	-	0.28	0.26	0.30	68	459131	169	33	129	7	195
CRW_00445	-	0.28	0.26	0.29	70	458165	178	24	144	10	195
CRW_00446	-	0.42	0.39	0.44	104	468762	140	16	114	10	161
CRW_00447	-	0.19	0.19	0.20	49	452433	207	33	161	13	211
CRW_00448	-	0.35	0.33	0.37	87	457211	166	26	122	18	174
CRW_00449	-	0.22	0.21	0.23	55	444853	191	24	164	3	205
CRW_00450	-	0.34	0.31	0.37	82	458184	155	13	124	18	180
CRW_00451	-	0.23	0.22	0.24	57	457204	199	24	161	14	207
CRW_00452	-	0.37	0.35	0.39	93	453390	155	24	121	10	169
CRW_00453	-	0.30	0.28	0.32	74	452448	164	23	131	10	187
CRW_00456	-	0.45	0.42	0.48	111	470705	135	19	100	16	154
CRW_00457	-	0.32	0.31	0.34	81	467792	167	22	133	12	183
CRW_00458	-	0.35	0.34	0.37	90	464887	164	30	123	11	174
CRW_00459	-	0.29	0.27	0.31	71	462012	175	27	131	17	192
CRW_00462	-	0.38	0.36	0.41	93	458178	151	18	114	19	168
CRW_00463	-	0.36	0.35	0.37	90	445799	160	21	130	9	164
CRW_00464	-	0.39	0.36	0.42	95	462015	141	15	116	10	169
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.61	0.60	0.62	273	1116325	194	25	142	27	185
CRW_00522	-	0.18	0.19	0.17	145	3642803	725	127	575	23	637
CRW_00530	-	0.35	0.37	0.33	99	534795	217	51	150	16	169
CRW_00532	-	0.19	0.20	0.17	54	579117	268	65	190	13	211
CRW_00533	-	0.19	0.22	0.16	49	453325	263	90	164	9	170
CRW_00535	-	0.23	0.24	0.21	80	898096	325	72	222	31	248
CRW_00538	-	0.20	0.21	0.19	62	811841	294	70	202	22	238
CRW_00542	-	0.15	0.18	0.14	56	994342	387	102	255	30	261
CRW_00545	-	0.29	0.33	0.26	63	1343736	378	53	128	197	130
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.22	0.21	0.22	95	1094029	351	37	299	15	350
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.32	0.31	0.33	141	1119330	303	41	244	18	311
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.61	0.60	0.62	267	1098475	190	19	142	29	179
CRW_00594	-	0.15	0.16	0.14	63	1028433	428	50	349	29	332
CRW_00596	-	0.23	0.24	0.22	92	1024178	344	55	271	18	294
CRW_00597	-	0.24	0.25	0.23	101	1200032	387	51	291	45	310
CRW_00604	-	0.52	0.57	0.48	46	411682	216	14	36	166	35
CRW_00606	-	0.67	0.65	0.69	60	559066	262	4	23	235	32
CRW_00607	-	0.54	0.55	0.53	42	536051	276	8	29	239	35
CRW_00615	-	0.50	0.57	0.44	47	553770	285	24	37	224	35
CRW_00617	-	0.69	0.69	0.69	44	426362	237	1	19	217	20
CRW_00678	-	0.42	0.48	0.37	58	666280	305	27	70	208	63
CRW_00680	-	0.30	0.34	0.27	41	516483	253	27	85	141	81
CRW_00683	-	0.44	0.47	0.41	63	460166	242	29	62	151	72
CRW_00684	-	0.36	0.39	0.33	53	612010	296	36	72	188	82
CRW_00702	-	0.66	0.72	0.61	54	357346	213	10	25	178	21
CRW_00704	-	0.81	0.80	0.82	75	386669	195	4	12	179	19
CRW_00706	-	0.46	0.51	0.42	30	695538	341	7	35	299	29
CRW_00710	-	0.70	0.70	0.69	80	1040287	377	8	28	341	34
CRW_00712	-	0.47	0.54	0.41	58	952749	371	28	55	288	50
CRW_00713	-	0.65	0.65	0.65	66	731343	308	11	25	272	35
CRW_00730	-	0.46	0.51	0.42	82	338879	185	33	82	70	79
CRW_00734	-	0.21	0.29	0.15	32	536958	260	99	77	84	78
CRW_00735	-	0.26	0.34	0.20	41	677825	298	90	74	134	80
CRW_00740	-	0.00	0.00	0.00	0	489333	296	100	122	74	113
CRW_00745	-	0.45	0.52	0.40	80	1343779	394	47	74	273	74
CRW_00746	-	0.42	0.43	0.40	95	550488	210	34	108	68	124
CRW_00750	-	0.25	0.29	0.21	46	709621	315	51	118	146	114
CRW_00751	-	0.57	0.62	0.53	110	489348	185	36	61	88	68
CRW_00753	-	0.15	0.16	0.13	29	489339	268	49	138	81	149
CRW_00757	-	0.08	0.10	0.07	13	415225	258	65	113	80	113
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.20	0.20	0.21	90	1215581	387	50	299	38	356
CRW_00765	-	0.24	0.24	0.24	62	452416	208	35	163	10	195
CRW_00766	-	0.22	0.22	0.23	52	440169	187	23	147	17	188
CRW_00768	-	0.60	0.58	0.62	150	471663	116	14	79	23	109
CRW_00769	-	0.40	0.37	0.42	94	451502	146	20	109	17	158
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.24	0.24	0.25	97	945607	320	41	255	24	307
CRW_00773	-	0.34	0.34	0.33	88	451460	186	30	147	9	171
CRW_00774	-	0.35	0.33	0.38	87	488335	169	17	127	25	176
CRW_00777	-	0.30	0.31	0.29	93	719076	260	47	184	29	211
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.22	0.22	0.22	84	1201649	346	41	251	54	300
CRW_00779	-	0.25	0.25	0.25	104	1031342	333	41	279	13	318
CRW_00780	-	0.32	0.31	0.34	79	475565	169	23	133	13	176
CRW_00783	-	0.31	0.31	0.31	80	453374	183	18	156	9	179
CRW_00784	-	0.34	0.33	0.36	86	456250	171	32	122	17	176
CRW_00785	-	0.35	0.33	0.36	84	452443	161	27	122	12	169
CRW_00787	-	0.26	0.26	0.26	81	646638	256	41	193	22	225
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.35	0.35	0.35	156	1137342	304	48	240	16	291
CRW_00793	-	0.25	0.26	0.24	97	1048678	351	44	257	50	280
CRW_00794	-	0.24	0.24	0.24	58	434539	200	18	163	19	188
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.24	0.25	0.23	98	1152503	357	51	269	37	296
CRW_00796	-	0.25	0.24	0.26	57	384786	182	29	131	22	178
CRW_00797	-	0.22	0.23	0.22	79	692890	299	41	243	15	263
CRW_00800	SSU_rRNA_eukarya links to Rfam database...	0.52	0.52	0.52	243	1401506	288	31	195	62	227
CRW_00801	-	0.45	0.45	0.45	111	438269	150	33	103	14	138
CRW_00802	-	0.31	0.30	0.31	76	460076	184	36	132	16	177
CRW_00807	-	0.39	0.39	0.39	157	1391544	337	46	199	92	241
CRW_00808	-	0.31	0.33	0.29	117	1301289	391	68	217	106	239
CRW_00813	-	0.20	0.23	0.17	31	530781	292	52	101	139	102
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.48	0.48	0.49	225	1117798	260	25	212	23	245
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.52	0.52	0.52	239	1135819	238	24	196	18	225
CRW_01134	-	0.28	0.28	0.28	119	964927	318	32	277	9	308
CRW_01168	-	0.38	0.38	0.38	156	900738	277	34	225	18	255
CRW_01186	-	0.27	0.27	0.27	104	836186	293	35	246	12	282
CRW_01188	-	0.19	0.19	0.19	76	837466	330	48	275	7	317
CRW_01189	-	0.22	0.22	0.21	87	862232	338	49	273	16	305
CRW_01214	-	0.34	0.34	0.35	136	931909	261	42	208	11	269
CRW_01222	-	0.25	0.25	0.25	98	912881	302	58	239	5	299
CRW_01224	-	0.37	0.37	0.38	145	912893	247	26	212	9	252
CRW_01239	-	0.23	0.23	0.23	87	840080	307	46	243	18	295
CRW_01250	-	0.24	0.24	0.24	89	781505	291	39	242	10	289
CRW_01260	-	0.17	0.17	0.17	66	912885	337	46	279	12	327
CRW_01266	-	0.27	0.28	0.27	105	818167	301	42	246	13	276
CRW_01271	-	0.30	0.30	0.30	116	827149	289	35	241	13	265
CRW_01275	-	0.39	0.39	0.39	169	1082226	281	38	223	20	263
CRW_01283	-	0.39	0.39	0.40	161	963559	264	37	209	18	248
CRW_01314	-	0.25	0.25	0.26	101	937377	297	39	248	10	306
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.34	0.33	0.34	145	977474	293	46	236	11	289
CRW_01344	-	0.33	0.33	0.34	120	791554	252	45	192	15	246
PDB_00409	-	0.28	0.32	0.24	79	688221	321	66	185	70	166
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.50	0.48	0.53	239	1073392	239	21	193	25	256
PDB_00805	-	0.69	0.67	0.71	201	467744	108	13	70	25	101
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.51	0.50	0.52	269	1433453	278	27	222	29	271
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.48	0.45	0.51	239	1204657	247	27	205	15	288
PDB_01261	-	0.50	0.45	0.55	152	467752	128	4	120	4	184
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.47	0.46	0.49	225	1117799	263	23	213	27	266

^top

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 ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

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

Performance of PknotsRG - scored lower in this pairwise comparison

1. Total counts & total scores for PknotsRG

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