CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAalifold(seed)		Sfold
MCC	0.744	>	0.480
Average MCC ± 95% Confidence Intervals	0.742 ± 0.039	>	0.479 ± 0.031
Sensitivity	0.678	>	0.422
Positive Predictive Value	0.818	>	0.545
Total TP	21759	>	13563
Total TN	85766748	<	85768490
Total FP	5870	<	13012
Total FP CONTRA	1107	<	1686
Total FP INCONS	3750	<	9625
Total FP COMP	1013	<	1701
Total FN	10343	<	18539
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RNAalifold(seed) and Sfold. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for RNAalifold(seed) and Sfold).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for RNAalifold(seed) and Sfold).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(seed) and Sfold. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for RNAalifold(seed) and Sfold).

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Performance of RNAalifold(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for RNAalifold(seed)

Total Base Pair Counts
Total TP	21759
Total TN	85766748
Total FP	5870
Total FP CONTRA	1107
Total FP INCONS	3750
Total FP COMP	1013
Total FN	10343

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

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2. Individual counts for RNAalifold(seed) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00024	SSU_rRNA_archaea links to Rfam database...	0.87	0.84	0.90	385	1085175	58	7	34	17	73
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.82	0.77	0.88	363	1141905	62	14	34	14	111
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.88	372	1170793	59	16	34	9	98
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.84	0.81	0.88	369	1107397	60	16	34	10	87
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.82	0.78	0.88	367	1172327	61	16	36	9	106
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.82	0.77	0.88	367	1181535	61	16	35	10	109
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.85	0.81	0.88	370	1108886	58	15	34	9	87
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.89	368	1178465	61	12	35	14	97
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.83	0.79	0.87	367	1135858	62	16	37	9	96
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.88	369	1201606	61	16	34	11	107
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	368	1152515	47	13	25	9	98
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	372	1180006	46	13	25	8	99
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.88	365	1190782	64	12	37	15	103
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.79	0.76	0.84	336	1082254	76	16	50	10	109
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.82	0.77	0.87	364	1178460	66	16	40	10	109
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.82	0.77	0.87	365	1207815	63	16	39	8	110
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.83	0.77	0.88	369	1198508	59	15	34	10	109
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.84	0.81	0.88	366	1105912	60	16	34	10	87
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.82	0.76	0.88	369	1218720	61	16	36	9	115
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.82	0.77	0.88	369	1198505	61	16	36	9	109
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	369	1192333	48	13	25	10	99
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.84	0.81	0.88	368	1111868	59	15	35	9	87
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.90	359	1122350	51	13	29	9	103
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.84	0.80	0.87	358	1085191	60	16	36	8	88
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.84	0.80	0.88	366	1114854	59	16	35	8	91
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.83	0.79	0.87	359	1110382	64	17	37	10	94
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.88	349	1129861	58	13	33	12	101
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.91	372	1180005	54	13	26	15	92
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.84	0.80	0.89	363	1117851	59	13	33	13	90
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.91	372	1144932	48	13	24	11	92
CRW_00283	SSU_rRNA_bacteria links to Rfam database...	0.80	0.75	0.85	323	1015644	67	14	44	9	109
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.89	356	1131358	59	13	33	13	100
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.82	0.78	0.86	356	1117847	66	17	40	9	102
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.80	0.75	0.86	358	1189235	67	16	44	7	118
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.77	0.71	0.84	329	1123856	76	14	51	11	132
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.45	0.39	0.52	178	1445508	175	32	132	11	284
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.44	0.37	0.53	184	1627762	174	32	132	10	318
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.44	0.36	0.53	184	1675017	173	32	132	9	323
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.42	0.36	0.51	172	1579413	180	32	136	12	310
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.44	0.36	0.52	181	1611565	175	31	133	11	315
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.44	0.37	0.53	184	1625958	174	32	132	10	314
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.40	0.32	0.50	169	2126616	180	32	136	12	365
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.44	0.35	0.55	182	1750923	164	28	123	13	333
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.45	0.38	0.55	186	1615165	163	28	124	11	310
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.45	0.37	0.54	182	1665890	171	28	125	18	313
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.86	0.82	0.91	377	1116350	49	12	26	11	81
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.86	0.81	0.92	361	1094068	53	6	25	22	84
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.92	366	1119360	52	6	24	22	86
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.92	365	1098507	56	8	23	25	81
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.41	0.34	0.49	163	1636811	183	35	136	12	318
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.85	0.78	0.92	348	1215641	59	6	25	28	98
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.81	0.75	0.88	302	945656	72	5	37	30	102
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.86	0.81	0.91	312	1201683	85	4	26	55	72
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	355	1137395	59	8	28	23	92
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.78	0.73	0.84	288	1152577	109	10	46	53	106
CRW_00800	SSU_rRNA_eukarya links to Rfam database...	0.42	0.33	0.52	156	1401675	160	25	119	16	314
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.82	0.76	0.88	356	1117856	63	14	34	15	114
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.84	0.80	0.88	372	1135856	59	15	35	9	92
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.41	0.34	0.49	172	1606179	193	36	141	16	331
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.43	0.36	0.52	181	1593657	177	34	133	10	325
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.83	0.79	0.88	344	977508	71	5	44	22	90
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.78	0.69	0.87	344	1073448	73	7	46	20	151
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.74	0.64	0.87	342	1500383	85	10	43	32	193
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.73	0.63	0.86	342	1471073	85	8	47	30	205
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.74	0.63	0.87	355	1606120	72	10	43	19	207
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.76	0.66	0.88	355	1433566	72	7	43	22	185
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.77	0.68	0.87	358	1204715	73	7	48	18	169
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.78	0.70	0.86	346	1117856	80	13	45	22	145

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Performance of Sfold - scored lower in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP	13563
Total TN	85768490
Total FP	13012
Total FP CONTRA	1686
Total FP INCONS	9625
Total FP COMP	1701
Total FN	18539

Total Scores
MCC	0.480
Average MCC ± 95% Confidence Intervals	0.479 ± 0.031
Sensitivity	0.422
Positive Predictive Value	0.545
Nr of predictions	68

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00024	SSU_rRNA_archaea links to Rfam database...	0.80	0.77	0.83	352	1085176	112	13	60	39	106
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.65	0.64	0.66	304	1141856	180	27	129	24	170
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.50	0.45	0.54	213	1170824	198	17	161	20	257
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.48	0.43	0.54	195	1107453	185	23	145	17	261
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.54	0.49	0.60	232	1172361	169	19	134	16	241
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.49	0.45	0.54	215	1181555	193	31	152	10	261
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.48	0.43	0.53	196	1108938	184	19	152	13	261
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.59	0.55	0.63	258	1178469	180	16	137	27	207
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.66	0.60	0.73	280	1135893	125	10	95	20	183
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.63	0.57	0.70	272	1201636	139	16	101	22	204
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.40	0.37	0.44	171	1152531	233	30	189	14	295
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.67	0.61	0.74	287	1180029	118	21	79	18	184
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.54	0.47	0.61	221	1190832	160	15	128	17	247
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.36	0.32	0.39	144	1082291	233	16	205	12	301
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.45	0.41	0.50	195	1178491	206	27	167	12	278
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.47	0.44	0.50	210	1207811	232	23	191	18	265
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.61	0.53	0.70	254	1198565	129	7	100	22	224
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.54	0.45	0.66	202	1106023	115	16	87	12	251
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.58	0.57	0.59	274	1218677	223	21	169	33	210
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.50	0.46	0.54	221	1198516	206	28	161	17	257
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.37	0.33	0.42	155	1192370	232	35	180	17	313
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.48	0.39	0.59	178	1111985	137	19	104	14	277
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.49	0.43	0.57	198	1122402	170	32	119	19	264
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.55	0.50	0.61	224	1085232	162	22	123	17	222
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.58	0.47	0.73	213	1114978	98	14	66	18	244
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.40	0.30	0.54	136	1110544	127	18	97	12	317
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.51	0.37	0.70	166	1130018	88	6	66	16	284
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.61	0.54	0.69	252	1180052	131	20	92	19	212
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.60	0.55	0.66	250	1117881	149	21	108	20	203
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.68	0.60	0.77	279	1144977	109	11	74	24	185
CRW_00283	SSU_rRNA_bacteria links to Rfam database...	0.31	0.24	0.40	102	1015772	167	19	132	16	330
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.42	0.33	0.53	149	1131480	147	20	111	16	307
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.77	0.71	0.83	326	1117866	94	16	52	26	132
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.59	0.51	0.68	241	1189298	141	19	95	27	235
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.36	0.31	0.41	142	1123904	219	35	169	15	319
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.21	0.19	0.24	88	1445476	332	57	229	46	374
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.46	0.37	0.56	187	1627778	175	32	113	30	315
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.38	0.33	0.43	166	1674980	241	44	175	22	341
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.36	0.35	0.36	169	1579286	334	74	224	36	313
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.38	0.34	0.42	171	1611504	271	50	185	36	325
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.39	0.35	0.45	172	1625925	245	34	175	36	326
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.44	0.34	0.58	183	2126636	205	17	117	71	351
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.29	0.27	0.31	138	1750806	345	60	252	33	377
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.39	0.32	0.47	157	1615171	217	28	147	42	339
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.33	0.29	0.38	146	1665840	278	40	199	39	349
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.57	0.54	0.61	247	1116358	185	18	142	25	211
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.31	0.26	0.36	116	1094139	220	19	186	15	329
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.58	0.40	0.84	179	1119542	50	5	30	15	273
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.60	0.56	0.65	248	1098523	153	22	110	21	198
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.23	0.22	0.25	105	1636722	354	42	276	36	376
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.33	0.28	0.40	124	1215709	234	16	171	47	322
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.30	0.27	0.34	108	945681	233	27	184	22	296
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.42	0.29	0.62	111	1201847	113	3	64	46	273
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.40	0.34	0.46	152	1137458	193	30	146	17	295
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.19	0.17	0.20	68	1152586	311	44	223	44	326
CRW_00800	SSU_rRNA_eukarya links to Rfam database...	0.52	0.46	0.59	215	1401613	204	32	115	57	255
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.50	0.48	0.52	227	1117826	230	18	189	23	243
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.59	0.52	0.66	241	1135913	144	19	105	20	223
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.37	0.30	0.45	152	1606193	221	35	148	38	351
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.33	0.29	0.38	149	1593608	285	55	193	37	357
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.37	0.34	0.41	147	977541	224	31	182	11	287
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.52	0.46	0.58	229	1073451	189	12	153	24	266
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.54	0.49	0.60	263	1500337	220	22	156	42	272
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.38	0.32	0.47	173	1471098	222	33	166	23	374
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.56	0.50	0.63	280	1606082	191	20	146	25	282
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.60	0.53	0.67	288	1433540	169	14	129	26	252
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.55	0.44	0.70	230	1204799	110	12	87	11	297
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.50	0.46	0.54	227	1117836	223	19	178	26	264

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Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.

Table of contents:

Overview

Performance plots

Performance of RNAalifold(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for RNAalifold(seed)

2. Individual counts for RNAalifold(seed) [ download as .csv ]

Performance of Sfold - scored lower in this pairwise comparison

1. Total counts & total scores for Sfold

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