CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	IPknot		PknotsRG
MCC	0.504	>	0.363
Average MCC ± 95% Confidence Intervals	0.497 ± 0.026	>	0.364 ± 0.022
Sensitivity	0.422	>	0.363
Positive Predictive Value	0.603	>	0.363
Total TP	23263	>	19991
Total TN	137623866	>	137607460
Total FP	21021	<	42527
Total FP CONTRA	2609	<	5822
Total FP INCONS	12725	<	29190
Total FP COMP	5687	<	7515
Total FN	31869	<	35141
P-value	3.56938820447e-08

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Performance plots

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

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Performance of IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	23263
Total TN	137623866
Total FP	21021
Total FP CONTRA	2609
Total FP INCONS	12725
Total FP COMP	5687
Total FN	31869

Total Scores
MCC	0.504
Average MCC ± 95% Confidence Intervals	0.497 ± 0.026
Sensitivity	0.422
Positive Predictive Value	0.603
Nr of predictions	168

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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_00002	-	0.64	0.53	0.77	139	408879	64	18	24	22	125
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_00338	-	0.21	0.20	0.23	79	1053084	273	64	199	10	316
CRW_00381	-	0.42	0.34	0.51	191	2303353	262	31	156	75	366
CRW_00417	-	0.43	0.36	0.52	95	458219	97	18	71	8	167
CRW_00418	-	0.34	0.23	0.50	60	441209	66	5	56	5	200
CRW_00419	-	0.38	0.28	0.52	73	464026	72	7	60	5	192
CRW_00421	-	0.53	0.39	0.72	103	463060	53	4	36	13	163
CRW_00422	-	0.48	0.37	0.64	96	455385	74	8	46	20	167
CRW_00424	-	0.42	0.32	0.55	117	789184	104	10	85	9	246
CRW_00426	-	0.34	0.28	0.41	75	457262	117	15	94	8	190
CRW_00427	-	0.29	0.25	0.35	64	454397	126	20	100	6	197
CRW_00428	-	0.48	0.37	0.64	95	465946	65	11	43	11	165
CRW_00430	-	0.38	0.27	0.55	71	456361	67	8	50	9	195
CRW_00433	-	0.35	0.24	0.53	63	467908	59	3	54	2	200
CRW_00434	-	0.41	0.29	0.57	77	457310	60	10	49	1	186
CRW_00435	-	0.35	0.26	0.48	68	451584	77	6	67	4	197
CRW_00437	-	0.32	0.24	0.42	62	456344	92	9	75	8	198
CRW_00438	-	0.44	0.34	0.56	92	454416	83	8	65	10	176
CRW_00441	-	0.30	0.20	0.44	52	454463	69	13	53	3	210
CRW_00442	-	0.40	0.31	0.52	81	453471	81	13	63	5	180
CRW_00443	-	0.33	0.23	0.46	61	456358	81	9	62	10	199
CRW_00444	-	0.43	0.30	0.60	80	459228	59	5	48	6	183
CRW_00445	-	0.36	0.28	0.46	74	458242	92	11	76	5	191
CRW_00446	-	0.40	0.34	0.47	90	468803	112	14	89	9	175
CRW_00447	-	0.36	0.28	0.47	73	452521	91	10	72	9	187
CRW_00448	-	0.44	0.30	0.67	77	457331	46	7	31	8	184
CRW_00449	-	0.34	0.23	0.49	61	444971	65	6	58	1	199
CRW_00450	-	0.33	0.24	0.45	62	458265	89	11	65	13	200
CRW_00451	-	0.39	0.31	0.49	81	457279	94	10	76	8	183
CRW_00452	-	0.39	0.29	0.54	75	453490	77	8	55	14	187
CRW_00453	-	0.37	0.27	0.51	70	452540	75	7	59	9	191
CRW_00456	-	0.44	0.31	0.61	83	470798	60	10	44	6	182
CRW_00457	-	0.51	0.42	0.61	111	467846	86	13	58	15	153
CRW_00458	-	0.53	0.42	0.67	112	464963	60	6	49	5	152
CRW_00459	-	0.58	0.44	0.76	115	462090	50	5	31	14	148
CRW_00462	-	0.41	0.29	0.58	76	458271	66	6	50	10	185
CRW_00463	-	0.43	0.36	0.51	92	445860	95	22	66	7	162
CRW_00464	-	0.49	0.30	0.81	78	462145	24	1	17	6	186
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.81	0.75	0.88	344	1116375	69	10	36	23	114
CRW_00522	-	0.32	0.26	0.39	201	3643140	326	51	258	17	581
CRW_00530	-	0.34	0.26	0.45	71	534937	94	30	57	7	197
CRW_00532	-	0.24	0.17	0.33	46	579285	103	22	73	8	219
CRW_00533	-	0.50	0.42	0.59	91	453474	81	19	44	18	128
CRW_00535	-	0.33	0.29	0.37	96	898207	180	41	126	13	232
CRW_00538	-	0.34	0.25	0.46	76	812010	109	15	74	20	224
CRW_00542	-	0.20	0.18	0.23	56	994513	218	44	142	32	261
CRW_00545	-	0.31	0.28	0.35	55	1343821	197	26	78	93	138
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_00594	-	0.35	0.29	0.41	115	1028615	180	23	142	15	280
CRW_00596	-	0.32	0.28	0.35	110	1024285	218	26	175	17	276
CRW_00597	-	0.26	0.25	0.28	101	1200110	295	30	234	31	310
CRW_00604	-	0.89	0.86	0.91	70	411701	129	5	2	122	11
CRW_00606	-	0.89	0.85	0.94	78	559070	188	0	5	183	14
CRW_00607	-	0.76	0.73	0.80	56	536060	259	10	4	245	21
CRW_00615	-	0.86	0.77	0.95	63	553812	211	0	3	208	19
CRW_00617	-	0.48	0.45	0.52	29	426370	178	4	23	151	35
CRW_00678	-	0.59	0.58	0.60	70	666319	212	9	37	166	51
CRW_00680	-	0.68	0.69	0.67	84	516510	190	13	29	148	38
CRW_00683	-	0.65	0.62	0.69	84	460198	151	11	27	113	51
CRW_00684	-	0.58	0.53	0.63	72	612057	178	14	28	136	63
CRW_00702	-	0.86	0.83	0.89	62	357365	141	7	1	133	13
CRW_00704	-	0.91	0.90	0.92	85	386668	146	4	3	139	9
CRW_00706	-	0.64	0.69	0.59	41	695540	219	11	18	190	18
CRW_00710	-	0.77	0.67	0.89	76	1040318	214	1	8	205	38
CRW_00712	-	0.78	0.76	0.80	82	952787	274	3	18	253	26
CRW_00713	-	0.84	0.76	0.93	77	731362	240	1	5	234	24
CRW_00730	-	0.46	0.45	0.46	73	338918	141	20	65	56	88
CRW_00734	-	0.62	0.48	0.80	53	537100	84	2	11	71	57
CRW_00735	-	0.54	0.49	0.60	59	677931	126	11	29	86	62
CRW_00740	-	0.02	0.03	0.02	3	489422	159	62	68	29	110
CRW_00745	-	0.73	0.72	0.73	111	1343828	207	15	26	166	43
CRW_00746	-	0.64	0.59	0.70	129	550542	110	18	36	56	90
CRW_00750	-	0.58	0.57	0.60	91	709684	186	19	42	125	69
CRW_00751	-	0.80	0.74	0.86	132	489402	79	12	9	58	46
CRW_00753	-	0.17	0.15	0.20	27	489421	156	27	80	49	151
CRW_00757	-	0.14	0.13	0.14	17	415291	164	36	72	56	109
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.48	0.34	0.67	153	1215790	109	10	67	32	293
CRW_00765	-	0.46	0.37	0.57	96	452509	76	13	58	5	161
CRW_00766	-	0.32	0.24	0.44	57	440262	83	10	62	11	183
CRW_00768	-	0.59	0.47	0.73	122	471740	54	6	38	10	137
CRW_00769	-	0.56	0.46	0.66	117	451549	68	12	47	9	135
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.44	0.34	0.57	136	945760	126	16	88	22	268
CRW_00773	-	0.42	0.37	0.48	95	451526	109	19	85	5	164
CRW_00774	-	0.50	0.35	0.72	93	488436	52	4	33	15	170
CRW_00777	-	0.40	0.34	0.47	102	719185	131	23	90	18	202
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.42	0.29	0.60	111	1201840	104	12	62	30	273
CRW_00779	-	0.45	0.39	0.51	164	1031447	169	24	131	14	258
CRW_00780	-	0.29	0.21	0.39	54	475662	88	18	66	4	201
CRW_00783	-	0.32	0.22	0.45	58	453499	79	9	62	8	201
CRW_00784	-	0.34	0.27	0.43	70	456326	105	18	76	11	192
CRW_00785	-	0.46	0.34	0.61	86	452536	58	8	46	4	167
CRW_00787	-	0.39	0.32	0.49	97	646753	108	19	84	5	209
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.55	0.46	0.66	206	1137473	121	11	96	14	241
CRW_00793	-	0.64	0.52	0.79	195	1048829	114	14	38	62	182
CRW_00794	-	0.37	0.28	0.49	68	434640	81	10	60	11	178
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.36	0.26	0.50	102	1152715	143	20	84	39	292
CRW_00796	-	0.28	0.19	0.43	44	384901	70	6	52	12	191
CRW_00797	-	0.37	0.28	0.49	97	693054	121	12	90	19	245
CRW_00800	SSU_rRNA_eukarya links to Rfam database...	0.62	0.51	0.75	240	1401657	117	12	66	39	230
CRW_00801	-	0.44	0.39	0.49	96	438322	108	21	77	10	153
CRW_00802	-	0.41	0.32	0.52	82	460161	86	14	63	9	171
CRW_00807	-	0.57	0.42	0.77	168	1391727	109	4	47	58	230
CRW_00808	-	0.29	0.21	0.39	75	1301498	175	36	82	57	281
CRW_00813	-	0.47	0.44	0.49	59	530845	179	12	49	118	74
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_01134	-	0.39	0.28	0.55	119	965137	105	17	82	6	308
CRW_01168	-	0.51	0.42	0.62	174	900872	124	17	90	17	237
CRW_01186	-	0.43	0.34	0.55	133	836328	116	15	95	6	253
CRW_01188	-	0.23	0.20	0.27	77	837582	210	31	175	4	316
CRW_01189	-	0.25	0.23	0.28	90	862315	245	36	200	9	302
CRW_01214	-	0.44	0.30	0.64	123	932102	77	10	60	7	282
CRW_01222	-	0.34	0.27	0.44	108	913029	140	28	111	1	289
CRW_01224	-	0.37	0.28	0.49	111	913048	125	14	103	8	286
CRW_01239	-	0.26	0.20	0.35	76	840237	144	22	121	1	306
CRW_01250	-	0.39	0.33	0.47	123	781612	152	20	120	12	255
CRW_01260	-	0.21	0.15	0.29	60	913066	164	21	129	14	333
CRW_01266	-	0.42	0.36	0.50	136	818290	147	12	122	13	245
CRW_01271	-	0.48	0.40	0.56	153	827269	128	20	99	9	228
CRW_01275	-	0.39	0.33	0.47	142	1082355	170	34	125	11	290
CRW_01283	-	0.37	0.31	0.45	126	963684	171	17	139	15	283
CRW_01314	-	0.32	0.27	0.39	109	937487	176	23	146	7	298
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.50	0.42	0.59	182	977595	134	16	108	10	252
CRW_01344	-	0.38	0.30	0.47	110	791679	131	20	102	9	256
PDB_00409	-	0.33	0.37	0.30	91	688246	288	61	153	74	154
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.64	0.57	0.72	282	1073454	132	13	96	23	213
PDB_00805	-	0.68	0.57	0.81	172	467816	53	6	34	13	130
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_01261	-	0.68	0.55	0.84	185	467809	34	0	34	0	151
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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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 IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

2. Individual counts for IPknot [ 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 ]