CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Contrafold		PknotsRG
MCC	0.462	>	0.367
Average MCC ± 95% Confidence Intervals	0.469 ± 0.023	>	0.372 ± 0.022
Sensitivity	0.434	>	0.365
Positive Predictive Value	0.492	>	0.371
Total TP	22987	>	19297
Total TN	129195841	>	129190487
Total FP	30491	<	38949
Total FP CONTRA	3384	<	5010
Total FP INCONS	20323	<	27741
Total FP COMP	6784	>	6198
Total FN	29948	<	33638
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	22987
Total TN	129195841
Total FP	30491
Total FP CONTRA	3384
Total FP INCONS	20323
Total FP COMP	6784
Total FN	29948

Total Scores
MCC	0.462
Average MCC ± 95% Confidence Intervals	0.469 ± 0.023
Sensitivity	0.434
Positive Predictive Value	0.492
Nr of predictions	155

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00002	-	0.72	0.62	0.82	164	408861	79	5	30	44	100
CRW_00024	SSU_rRNA_archaea links to Rfam database...	0.77	0.77	0.78	351	1085153	140	12	85	43	107
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.68	0.68	0.68	320	1141844	188	22	130	36	154
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.60	0.57	0.64	268	1170795	174	25	127	22	202
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.54	0.52	0.56	237	1107395	202	25	159	18	219
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.64	0.60	0.67	286	1172318	164	20	122	22	187
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.59	0.58	0.61	274	1181504	188	29	146	13	202
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.51	0.51	0.53	231	1108865	226	32	177	17	226
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.55	0.53	0.57	245	1178450	213	19	166	28	220
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.56	0.52	0.61	243	1135878	175	14	143	18	220
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.62	0.60	0.64	287	1201577	192	19	142	31	189
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.55	0.51	0.59	237	1152519	185	22	143	20	229
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.53	0.49	0.57	233	1180006	196	22	155	19	238
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.62	0.59	0.64	277	1190763	182	19	137	26	191
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.34	0.34	0.35	150	1082228	288	32	246	10	295
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.50	0.48	0.52	228	1178444	227	20	188	19	245
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.57	0.55	0.59	259	1207798	197	27	151	19	216
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.54	0.52	0.56	250	1198476	220	27	173	20	228
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.53	0.51	0.55	229	1105912	212	23	164	25	224
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.64	0.62	0.66	301	1218683	200	21	136	43	183
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.58	0.56	0.61	267	1198490	184	24	145	15	211
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.47	0.44	0.50	206	1192327	232	26	181	25	262
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.66	0.63	0.69	286	1111874	157	20	106	31	169
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.51	0.48	0.53	221	1122337	215	30	163	22	241
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.47	0.46	0.49	203	1085190	233	20	188	25	243
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.61	0.59	0.63	271	1114843	186	19	138	29	186
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.44	0.40	0.49	182	1110423	203	23	167	13	271
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.44	0.42	0.47	190	1129849	240	28	189	23	260
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.60	0.56	0.64	262	1180004	173	25	125	23	202
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.55	0.51	0.60	232	1117873	173	15	140	18	221
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.64	0.62	0.65	288	1144901	182	17	135	30	176
CRW_00283	SSU_rRNA_bacteria links to Rfam database...	0.41	0.38	0.45	162	1015668	217	29	166	22	270
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.51	0.47	0.56	216	1131371	196	24	149	23	240
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.66	0.63	0.68	289	1117836	159	19	116	24	169
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.60	0.57	0.63	270	1189221	197	21	141	35	206
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.38	0.36	0.40	165	1123842	258	35	208	15	296
CRW_00338	-	0.20	0.21	0.19	84	1052972	396	77	293	26	311
CRW_00381	-	0.40	0.38	0.41	214	2303211	410	37	269	104	343
CRW_00417	-	0.41	0.38	0.44	99	458178	135	23	103	9	163
CRW_00418	-	0.26	0.22	0.31	56	441150	130	14	110	6	204
CRW_00419	-	0.40	0.35	0.45	93	463958	122	7	108	7	172
CRW_00421	-	0.50	0.44	0.57	117	462998	111	10	78	23	149
CRW_00422	-	0.44	0.40	0.49	105	455320	131	13	97	21	158
CRW_00424	-	0.49	0.45	0.52	164	789083	172	18	131	23	199
CRW_00426	-	0.42	0.39	0.45	103	457219	137	13	111	13	162
CRW_00427	-	0.28	0.26	0.29	69	454346	182	30	136	16	192
CRW_00428	-	0.37	0.33	0.40	87	465879	144	17	112	15	173
CRW_00430	-	0.39	0.32	0.48	85	456313	101	17	75	9	181
CRW_00433	-	0.33	0.28	0.40	73	467844	115	12	99	4	190
CRW_00434	-	0.48	0.40	0.56	106	457257	91	9	74	8	157
CRW_00435	-	0.30	0.26	0.34	68	451527	139	21	109	9	197
CRW_00437	-	0.25	0.22	0.29	57	456294	151	16	123	12	203
CRW_00438	-	0.39	0.34	0.44	92	454372	126	15	102	9	176
CRW_00441	-	0.37	0.31	0.44	80	454400	110	12	89	9	182
CRW_00442	-	0.32	0.28	0.37	74	453426	139	14	114	11	187
CRW_00443	-	0.34	0.26	0.43	68	456333	107	8	81	18	192
CRW_00444	-	0.45	0.38	0.53	100	459174	99	15	72	12	163
CRW_00445	-	0.43	0.40	0.47	105	458179	127	19	100	8	160
CRW_00446	-	0.33	0.31	0.36	81	468771	157	18	126	13	184
CRW_00447	-	0.29	0.27	0.30	71	452442	174	23	140	11	189
CRW_00448	-	0.29	0.26	0.34	67	457247	143	23	109	11	194
CRW_00449	-	0.42	0.37	0.48	95	444897	111	20	84	7	165
CRW_00450	-	0.43	0.36	0.53	94	458224	101	11	74	16	168
CRW_00451	-	0.43	0.38	0.49	99	457244	114	11	92	11	165
CRW_00452	-	0.49	0.41	0.59	108	453445	94	7	68	19	154
CRW_00453	-	0.38	0.32	0.44	84	452487	117	13	92	12	177
CRW_00456	-	0.45	0.37	0.56	98	470760	83	10	67	6	167
CRW_00457	-	0.44	0.41	0.48	107	467803	134	17	101	16	157
CRW_00458	-	0.48	0.42	0.54	111	464926	106	9	84	13	153
CRW_00459	-	0.52	0.46	0.58	121	462032	112	10	78	24	142
CRW_00462	-	0.46	0.40	0.53	104	458208	107	10	81	16	157
CRW_00463	-	0.44	0.40	0.49	101	445832	116	18	89	9	153
CRW_00464	-	0.46	0.38	0.55	101	462056	95	8	76	11	163
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.70	0.68	0.73	312	1116336	148	19	98	31	146
CRW_00522	-	0.32	0.30	0.33	238	3642926	513	86	400	27	544
CRW_00530	-	0.35	0.34	0.37	91	534848	170	47	109	14	177
CRW_00535	-	0.37	0.37	0.38	121	898149	221	45	155	21	207
CRW_00538	-	0.41	0.38	0.45	113	811923	164	23	116	25	187
CRW_00542	-	0.28	0.30	0.27	95	994401	299	70	189	40	222
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.33	0.30	0.36	134	1094090	257	24	212	21	311
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.36	0.35	0.38	157	1119345	281	41	213	27	295
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.62	0.60	0.65	268	1098489	182	28	118	36	178
CRW_00594	-	0.23	0.24	0.22	96	1028467	363	49	283	31	299
CRW_00596	-	0.24	0.25	0.24	95	1024193	335	44	264	27	291
CRW_00597	-	0.27	0.28	0.27	115	1200049	353	41	270	42	296
CRW_00604	-	0.84	0.85	0.82	69	411694	186	4	11	171	12
CRW_00606	-	0.93	0.90	0.97	83	559067	236	0	3	233	9
CRW_00607	-	0.81	0.82	0.81	63	536052	269	3	12	254	14
CRW_00615	-	0.86	0.85	0.88	70	553798	271	0	10	261	12
CRW_00617	-	0.57	0.55	0.60	35	426368	211	6	17	188	29
CRW_00678	-	0.42	0.44	0.40	53	666302	315	14	66	235	68
CRW_00680	-	0.53	0.55	0.52	67	516506	229	17	46	166	55
CRW_00683	-	0.63	0.63	0.63	85	460186	216	2	47	167	50
CRW_00684	-	0.53	0.55	0.51	74	612025	266	16	56	194	61
CRW_00702	-	0.72	0.73	0.71	55	357357	187	7	16	164	20
CRW_00704	-	0.87	0.87	0.87	82	386666	195	4	8	183	12
CRW_00706	-	0.64	0.71	0.58	42	695537	308	13	18	277	17
CRW_00710	-	0.69	0.64	0.74	73	1040304	312	2	24	286	41
CRW_00712	-	0.44	0.48	0.39	52	952758	374	24	56	294	56
CRW_00713	-	0.80	0.77	0.84	78	731352	295	5	10	280	23
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.38	0.32	0.44	144	1215694	231	27	155	49	302
CRW_00765	-	0.43	0.39	0.47	101	452459	126	21	95	10	156
CRW_00766	-	0.27	0.23	0.31	56	440213	138	20	102	16	184
CRW_00768	-	0.61	0.55	0.68	143	471695	100	7	61	32	116
CRW_00769	-	0.48	0.43	0.53	108	451522	115	21	74	20	144
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.40	0.37	0.44	148	945666	215	18	168	29	256
CRW_00773	-	0.48	0.45	0.51	116	451497	135	19	93	23	143
CRW_00774	-	0.44	0.40	0.49	105	488352	131	8	101	22	158
CRW_00777	-	0.43	0.42	0.45	127	719119	199	27	127	45	177
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.52	0.45	0.59	174	1201730	163	16	105	42	210
CRW_00779	-	0.37	0.36	0.39	150	1031380	264	22	214	28	272
CRW_00780	-	0.32	0.29	0.35	74	475591	151	18	117	16	181
CRW_00783	-	0.39	0.33	0.45	86	453437	121	12	93	16	173
CRW_00784	-	0.41	0.37	0.45	96	456279	134	19	96	19	166
CRW_00785	-	0.54	0.48	0.62	122	452478	89	12	64	13	131
CRW_00787	-	0.49	0.45	0.53	138	646691	151	13	111	27	168
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.48	0.44	0.53	196	1137416	209	14	160	35	251
CRW_00793	-	0.54	0.50	0.59	189	1048753	210	26	108	76	188
CRW_00794	-	0.37	0.35	0.39	85	434558	154	20	115	19	161
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.35	0.33	0.38	131	1152575	263	22	193	48	263
CRW_00796	-	0.36	0.29	0.45	69	384851	109	2	81	26	166
CRW_00797	-	0.33	0.30	0.38	101	692984	189	25	143	21	241
CRW_00800	SSU_rRNA_eukarya links to Rfam database...	0.57	0.54	0.60	253	1401550	230	21	151	58	217
CRW_00801	-	0.47	0.45	0.49	113	438286	131	27	90	14	136
CRW_00802	-	0.42	0.39	0.45	99	460102	145	19	100	26	154
CRW_00807	-	0.52	0.47	0.56	188	1391613	233	14	131	88	210
CRW_00808	-	0.31	0.29	0.33	103	1301378	324	43	167	114	253
CRW_00813	-	0.44	0.47	0.41	63	530812	220	29	61	130	70
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.57	0.56	0.57	265	1117797	226	19	179	28	205
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.62	0.60	0.64	280	1135838	187	19	141	27	184
CRW_01134	-	0.38	0.35	0.41	148	964992	225	35	180	10	279
CRW_01168	-	0.50	0.48	0.53	196	900783	197	25	149	23	215
CRW_01186	-	0.40	0.38	0.42	146	836224	219	23	178	18	240
CRW_01188	-	0.20	0.20	0.20	77	837476	320	47	265	8	316
CRW_01189	-	0.23	0.23	0.23	92	862249	314	44	256	14	300
CRW_01214	-	0.30	0.28	0.32	114	931943	252	28	210	14	291
CRW_01222	-	0.30	0.28	0.33	113	912930	241	48	185	8	284
CRW_01224	-	0.40	0.36	0.45	141	912960	188	17	158	13	256
CRW_01239	-	0.24	0.23	0.25	88	840107	271	42	219	10	294
CRW_01250	-	0.45	0.41	0.49	155	781556	186	19	145	22	223
CRW_01260	-	0.23	0.20	0.25	80	912961	256	30	205	21	313
CRW_01266	-	0.35	0.35	0.34	134	818168	277	41	217	19	247
CRW_01271	-	0.32	0.32	0.32	121	827157	280	31	232	17	260
CRW_01275	-	0.38	0.37	0.40	160	1082251	264	41	204	19	272
CRW_01283	-	0.33	0.30	0.36	123	963626	238	25	192	21	286
CRW_01314	-	0.30	0.28	0.33	114	937422	242	30	199	13	293
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.46	0.44	0.48	189	977509	217	30	173	14	245
CRW_01344	-	0.28	0.27	0.30	98	791579	243	31	203	9	268
PDB_00409	-	0.35	0.40	0.30	99	688225	317	68	159	90	146
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.53	0.50	0.56	246	1073403	229	19	177	33	249
PDB_00805	-	0.66	0.64	0.68	193	467745	126	7	83	36	109
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.58	0.56	0.60	303	1433467	242	16	185	41	237
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.49	0.44	0.55	232	1204703	216	20	173	23	295
PDB_01261	-	0.79	0.69	0.90	233	467769	32	2	24	6	103
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.49	0.47	0.51	232	1117807	258	16	205	37	259

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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	19297
Total TN	129190487
Total FP	38949
Total FP CONTRA	5010
Total FP INCONS	27741
Total FP COMP	6198
Total FN	33638

Total Scores
MCC	0.367
Average MCC ± 95% Confidence Intervals	0.372 ± 0.022
Sensitivity	0.365
Positive Predictive Value	0.371
Nr of predictions	155

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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_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_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_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 Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

2. Individual counts for Contrafold [ 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 ]