CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAfold		PknotsRG
MCC	0.364	>	0.363
Average MCC ± 95% Confidence Intervals	0.364 ± 0.022	<	0.364 ± 0.022
Sensitivity	0.364	>	0.363
Positive Predictive Value	0.364	>	0.363
Total TP	20067	>	19991
Total TN	137607286	<	137607460
Total FP	42702	>	42527
Total FP CONTRA	5815	<	5822
Total FP INCONS	29295	>	29190
Total FP COMP	7592	>	7515
Total FN	35065	<	35141
P-value	0.00985919189012

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Performance plots

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

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Performance of RNAfold - scored higher in this pairwise comparison

1. Total counts & total scores for RNAfold

Total Base Pair Counts
Total TP	20067
Total TN	137607286
Total FP	42702
Total FP CONTRA	5815
Total FP INCONS	29295
Total FP COMP	7592
Total FN	35065

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

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00002	-	0.50	0.49	0.50	130	408802	144	31	97	16	134
CRW_00024	SSU_rRNA_archaea links to Rfam database...	0.78	0.76	0.79	350	1085158	132	17	76	39	108
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.63	0.63	0.63	300	1141838	201	31	147	23	174
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.35	0.35	0.36	164	1170755	315	33	263	19	306
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.53	0.52	0.54	238	1107379	215	34	165	16	218
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.60	0.60	0.61	283	1172280	205	23	160	22	190
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.53	0.53	0.53	252	1181474	240	37	190	13	224
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.46	0.46	0.46	210	1108845	266	27	223	16	247
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.47	0.47	0.47	220	1178412	266	29	219	18	245
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.59	0.58	0.59	270	1135819	209	32	157	20	193
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.59	0.58	0.61	277	1201568	204	13	167	24	199
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.39	0.38	0.39	179	1152463	296	36	243	17	287
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.54	0.53	0.55	249	1179962	229	32	173	24	222
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.47	0.46	0.47	217	1190733	262	26	220	16	251
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.29	0.29	0.29	131	1082204	330	37	284	9	314
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.42	0.42	0.42	197	1178408	288	34	241	13	276
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.44	0.44	0.44	208	1207762	286	29	236	21	267
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.56	0.54	0.57	259	1198471	217	29	167	21	219
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.39	0.39	0.39	176	1105876	287	34	242	11	277
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.57	0.57	0.58	276	1218664	233	24	177	32	208
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.40	0.40	0.40	190	1198454	296	51	231	14	288
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.41	0.41	0.42	190	1192286	279	40	224	15	278
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.38	0.37	0.40	170	1111856	279	38	222	19	285
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.49	0.48	0.50	224	1122302	241	35	190	16	238
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.55	0.54	0.55	240	1085168	217	29	164	24	206
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.50	0.49	0.51	226	1114829	235	24	192	19	231
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.37	0.37	0.37	169	1110340	304	41	245	18	284
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.42	0.41	0.43	186	1129828	264	31	211	22	264
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.35	0.34	0.35	157	1179973	303	36	250	17	307
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.50	0.49	0.50	222	1117818	233	28	192	13	231
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.30	0.30	0.29	138	1144872	346	41	290	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...	0.28	0.27	0.28	124	1131316	333	36	284	13	332
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.63	0.62	0.63	284	1117810	186	24	142	20	174
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.39	0.38	0.40	181	1189200	291	36	236	19	295
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.30	0.30	0.31	136	1123816	309	46	252	11	325
CRW_00338	-	0.14	0.15	0.13	60	1052948	422	74	344	4	335
CRW_00381	-	0.32	0.33	0.31	184	2303140	511	67	340	104	373
CRW_00417	-	0.38	0.37	0.39	97	458157	160	21	128	11	165
CRW_00418	-	0.21	0.20	0.23	51	441107	179	25	147	7	209
CRW_00419	-	0.22	0.21	0.23	55	463931	187	18	162	7	210
CRW_00421	-	0.34	0.32	0.36	86	462964	166	22	131	13	180
CRW_00422	-	0.26	0.25	0.28	65	455302	185	23	145	17	198
CRW_00424	-	0.38	0.38	0.37	138	789026	258	22	210	26	225
CRW_00426	-	0.40	0.38	0.41	102	457198	158	27	119	12	163
CRW_00427	-	0.21	0.21	0.22	54	454333	207	33	161	13	207
CRW_00428	-	0.39	0.38	0.40	98	465850	158	28	119	11	162
CRW_00430	-	0.22	0.21	0.23	56	456245	198	23	166	9	210
CRW_00433	-	0.29	0.26	0.33	69	467817	147	21	121	5	194
CRW_00434	-	0.39	0.36	0.42	94	457220	142	17	115	10	169
CRW_00435	-	0.32	0.30	0.33	80	451486	161	19	140	2	185
CRW_00437	-	0.21	0.21	0.22	54	456242	201	25	169	7	206
CRW_00438	-	0.35	0.34	0.37	90	454335	166	19	137	10	178
CRW_00441	-	0.25	0.23	0.27	61	454355	169	27	138	4	201
CRW_00442	-	0.37	0.36	0.39	94	453386	156	25	123	8	167
CRW_00443	-	0.39	0.36	0.42	93	456267	151	22	108	21	167
CRW_00444	-	0.25	0.24	0.27	63	459128	178	32	138	8	200
CRW_00445	-	0.26	0.25	0.28	65	458167	180	24	147	9	200
CRW_00446	-	0.52	0.49	0.56	131	468760	121	11	94	16	134
CRW_00447	-	0.30	0.28	0.31	74	452437	184	17	148	19	186
CRW_00448	-	0.35	0.34	0.37	88	457211	166	26	121	19	173
CRW_00449	-	0.28	0.27	0.29	71	444849	178	27	149	2	189
CRW_00450	-	0.32	0.30	0.34	78	458171	169	22	132	15	184
CRW_00451	-	0.21	0.20	0.21	52	457204	203	26	164	13	212
CRW_00452	-	0.26	0.25	0.28	66	453389	185	27	146	12	196
CRW_00453	-	0.27	0.25	0.29	65	452448	171	30	133	8	196
CRW_00456	-	0.45	0.42	0.48	112	470704	135	20	99	16	153
CRW_00457	-	0.34	0.32	0.37	85	467798	158	17	128	13	179
CRW_00458	-	0.37	0.35	0.38	93	464886	163	30	121	12	171
CRW_00459	-	0.29	0.27	0.31	72	462008	178	27	134	17	191
CRW_00462	-	0.14	0.13	0.14	34	458165	214	27	177	10	227
CRW_00463	-	0.28	0.28	0.29	71	445794	181	25	150	6	183
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	0.59	0.62	272	1116326	195	24	143	28	186
CRW_00522	-	0.25	0.26	0.24	202	3642812	663	123	513	27	580
CRW_00530	-	0.29	0.31	0.27	82	534794	236	54	165	17	186
CRW_00532	-	0.22	0.24	0.20	63	579111	278	65	187	26	202
CRW_00533	-	0.20	0.23	0.17	51	453327	258	88	162	8	168
CRW_00535	-	0.29	0.31	0.27	102	898090	299	76	202	21	226
CRW_00538	-	0.19	0.21	0.18	63	811827	305	77	208	20	237
CRW_00542	-	0.19	0.21	0.17	68	994343	375	98	246	31	249
CRW_00545	-	0.30	0.32	0.28	62	1343761	372	46	111	215	131
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.18	0.18	0.18	78	1094024	373	34	324	15	367
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.31	0.31	0.31	138	1119315	322	37	266	19	314
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.37	0.38	0.37	168	1098447	302	42	246	14	278
CRW_00594	-	0.23	0.25	0.21	98	1028436	387	54	307	26	297
CRW_00596	-	0.23	0.24	0.22	92	1024184	347	40	280	27	294
CRW_00597	-	0.24	0.25	0.23	101	1200028	392	49	297	46	310
CRW_00604	-	0.52	0.57	0.48	46	411682	217	15	35	167	35
CRW_00606	-	0.66	0.64	0.69	59	559067	263	2	25	236	33
CRW_00607	-	0.54	0.55	0.53	42	536050	277	8	30	239	35
CRW_00615	-	0.50	0.56	0.44	46	553773	284	24	35	225	36
CRW_00617	-	0.27	0.31	0.24	20	426343	263	19	44	200	44
CRW_00678	-	0.64	0.64	0.64	77	666315	276	10	33	233	44
CRW_00680	-	0.66	0.68	0.64	83	516507	213	8	38	167	39
CRW_00683	-	0.40	0.41	0.38	55	460177	239	20	68	151	80
CRW_00684	-	0.36	0.39	0.33	53	612010	292	37	71	184	82
CRW_00702	-	0.66	0.72	0.61	54	357347	206	10	24	172	21
CRW_00704	-	0.81	0.80	0.82	75	386669	196	4	12	180	19
CRW_00706	-	0.37	0.41	0.34	24	695540	344	7	39	298	35
CRW_00710	-	0.66	0.65	0.67	74	1040293	374	8	28	338	40
CRW_00712	-	0.47	0.54	0.42	58	952751	366	28	53	285	50
CRW_00713	-	0.67	0.65	0.69	66	731349	302	5	25	272	35
CRW_00730	-	0.46	0.53	0.40	86	338863	190	41	86	63	75
CRW_00734	-	0.16	0.22	0.11	24	536953	266	107	82	77	86
CRW_00735	-	0.29	0.37	0.22	45	677826	294	90	69	135	76
CRW_00740	-	0.07	0.10	0.06	11	489361	287	63	120	104	102
CRW_00745	-	0.45	0.53	0.39	81	1343774	396	51	74	271	73
CRW_00746	-	0.42	0.45	0.40	99	550475	223	33	118	72	120
CRW_00750	-	0.37	0.42	0.34	67	709636	300	37	96	167	93
CRW_00751	-	0.58	0.63	0.54	112	489347	183	36	60	87	66
CRW_00753	-	0.15	0.16	0.13	29	489339	272	47	140	85	149
CRW_00757	-	0.17	0.23	0.13	29	415185	257	108	94	55	97
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.22	0.21	0.22	95	1215590	376	51	284	41	351
CRW_00765	-	0.44	0.44	0.45	113	452424	156	21	118	17	144
CRW_00766	-	0.22	0.22	0.23	52	440167	190	20	152	18	188
CRW_00768	-	0.50	0.48	0.51	125	471661	142	15	105	22	134
CRW_00769	-	0.39	0.37	0.42	93	451501	148	21	110	17	159
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.25	0.24	0.25	98	945608	317	41	253	23	306
CRW_00773	-	0.34	0.34	0.33	88	451460	186	30	147	9	171
CRW_00774	-	0.27	0.27	0.28	70	488320	198	15	161	22	193
CRW_00777	-	0.24	0.25	0.23	77	719060	291	60	203	28	227
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.23	0.22	0.23	85	1201662	341	40	238	63	299
CRW_00779	-	0.24	0.24	0.24	103	1031342	335	40	281	14	319
CRW_00780	-	0.20	0.19	0.21	49	475564	199	20	167	12	206
CRW_00783	-	0.31	0.31	0.32	80	453377	182	16	155	11	179
CRW_00784	-	0.36	0.34	0.38	90	456253	169	22	125	22	172
CRW_00785	-	0.35	0.33	0.36	84	452443	161	27	122	12	169
CRW_00787	-	0.23	0.24	0.22	72	646627	264	41	213	10	234
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.36	0.36	0.36	161	1137337	307	44	244	19	286
CRW_00793	-	0.33	0.34	0.33	129	1048680	326	54	213	59	248
CRW_00794	-	0.24	0.24	0.24	58	434537	202	18	165	19	188
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.22	0.23	0.21	89	1152504	360	53	275	32	305
CRW_00796	-	0.20	0.20	0.21	47	384780	189	27	149	13	188
CRW_00797	-	0.22	0.23	0.21	79	692885	304	40	249	15	263
CRW_00800	SSU_rRNA_eukarya links to Rfam database...	0.48	0.47	0.48	223	1401508	313	43	201	69	247
CRW_00801	-	0.43	0.43	0.43	106	438270	153	32	108	13	143
CRW_00802	-	0.30	0.30	0.31	75	460080	183	33	132	18	178
CRW_00807	-	0.39	0.40	0.39	158	1391544	337	46	198	93	240
CRW_00808	-	0.31	0.33	0.29	118	1301289	392	68	216	108	238
CRW_00813	-	0.13	0.15	0.11	20	530775	316	43	127	146	113
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.48	0.48	0.48	225	1117795	263	20	220	23	245
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.62	0.61	0.62	282	1135826	195	25	145	25	182
CRW_01134	-	0.24	0.25	0.24	105	964918	338	37	295	6	322
CRW_01168	-	0.38	0.38	0.38	156	900739	276	35	223	18	255
CRW_01186	-	0.29	0.30	0.29	114	836184	292	36	237	19	272
CRW_01188	-	0.16	0.17	0.16	65	837463	344	53	284	7	328
CRW_01189	-	0.18	0.19	0.18	73	862243	341	43	282	16	319
CRW_01214	-	0.29	0.29	0.29	117	931897	291	28	253	10	288
CRW_01222	-	0.25	0.25	0.25	99	912875	309	56	246	7	298
CRW_01224	-	0.36	0.35	0.37	140	912901	245	27	208	10	257
CRW_01239	-	0.21	0.21	0.21	80	840073	320	44	259	17	302
CRW_01250	-	0.24	0.24	0.24	90	781502	295	38	245	12	288
CRW_01260	-	0.14	0.14	0.14	55	912875	359	52	294	13	338
CRW_01266	-	0.25	0.26	0.25	99	818161	313	44	256	13	282
CRW_01271	-	0.33	0.34	0.33	129	827149	276	38	225	13	252
CRW_01275	-	0.35	0.35	0.34	153	1082212	314	52	239	23	279
CRW_01283	-	0.32	0.31	0.32	126	963578	281	35	227	19	283
CRW_01314	-	0.24	0.23	0.24	95	937373	303	38	259	6	312
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.37	0.37	0.38	160	977476	278	42	223	13	274
CRW_01344	-	0.32	0.32	0.32	116	791548	261	44	203	14	250
PDB_00409	-	0.25	0.29	0.21	71	688215	334	71	194	69	174
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.48	0.46	0.51	228	1073395	247	19	203	25	267
PDB_00805	-	0.65	0.64	0.67	192	467742	117	17	77	23	110
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.48	0.47	0.49	254	1433456	289	27	234	28	286
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.45	0.43	0.47	228	1204646	269	31	223	15	299
PDB_01261	-	0.50	0.45	0.55	152	467750	130	4	122	4	184
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.49	0.47	0.50	232	1117800	256	26	202	28	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	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 RNAfold - scored higher in this pairwise comparison

1. Total counts & total scores for RNAfold

2. Individual counts for RNAfold [ 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 ]