CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MXScarna(seed)		Contrafold
MCC	0.659	>	0.513
Average MCC ± 95% Confidence Intervals	0.662 ± 0.026	>	0.512 ± 0.027
Sensitivity	0.589	>	0.489
Positive Predictive Value	0.738	>	0.538
Total TP	17728	>	14717
Total TN	79088306	>	79084976
Total FP	8922	<	14699
Total FP CONTRA	930	<	1711
Total FP INCONS	5363	<	10923
Total FP COMP	2629	>	2065
Total FN	12352	<	15363
P-value	3.56938820447e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	17728
Total TN	79088306
Total FP	8922
Total FP CONTRA	930
Total FP INCONS	5363
Total FP COMP	2629
Total FN	12352

Total Scores
MCC	0.659
Average MCC ± 95% Confidence Intervals	0.662 ± 0.026
Sensitivity	0.589
Positive Predictive Value	0.738
Nr of predictions	64

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2. Individual counts for MXScarna(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...	0.83	0.81	0.86	369	1085172	112	11	49	52	89
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.68	0.60	0.78	285	1141950	117	9	72	36	189
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.74	0.68	0.82	318	1170827	101	10	60	31	152
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.73	0.66	0.81	302	1107443	101	13	58	30	154
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.72	0.64	0.81	305	1172369	105	12	60	33	168
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.73	0.66	0.81	312	1181569	104	11	61	32	164
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.74	0.67	0.82	305	1108933	99	12	55	32	152
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.72	0.65	0.81	301	1178507	110	5	67	38	164
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.73	0.66	0.81	304	1135902	106	11	61	34	159
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.73	0.66	0.82	312	1201645	103	12	56	35	164
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.72	0.64	0.81	300	1152549	106	11	61	34	166
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.74	0.68	0.82	319	1180025	107	12	60	35	152
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.73	0.65	0.82	305	1190824	106	6	61	39	163
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.65	0.59	0.72	264	1082289	130	14	89	27	181
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.68	0.61	0.77	287	1178505	117	12	76	29	186
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.76	0.69	0.83	327	1207841	102	11	56	35	148
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.75	0.67	0.83	321	1198539	99	12	54	33	157
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.73	0.66	0.81	299	1105958	104	12	59	33	154
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.72	0.64	0.81	311	1218757	105	11	62	32	173
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.71	0.64	0.78	307	1198533	120	11	75	34	171
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.74	0.66	0.82	311	1192362	98	11	56	31	157
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.74	0.67	0.82	304	1111915	100	11	56	33	151
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.71	0.64	0.80	295	1122381	105	12	63	30	167
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.72	0.65	0.80	290	1085237	110	10	64	36	156
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.74	0.67	0.82	306	1114897	103	10	58	35	151
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.73	0.66	0.80	300	1110421	108	12	62	34	153
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.68	0.60	0.78	271	1129907	113	9	69	35	179
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.72	0.64	0.81	299	1180047	107	10	60	37	165
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.70	0.63	0.79	284	1117899	114	10	67	37	169
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.73	0.66	0.82	305	1144968	102	10	58	34	159
CRW_00283	SSU_rRNA_bacteria links to Rfam database...	0.63	0.56	0.71	242	1015684	127	13	86	28	190
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.73	0.65	0.81	297	1131394	104	10	59	35	159
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.71	0.64	0.79	294	1117886	113	13	67	33	164
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.68	0.60	0.77	287	1189280	118	12	74	32	189
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.62	0.53	0.71	245	1123906	126	12	87	27	216
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.42	0.39	0.46	181	1445456	267	46	167	54	281
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.48	0.45	0.51	215	1579331	275	41	166	68	267
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.50	0.47	0.53	232	1611469	276	42	167	67	264
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.36	0.32	0.41	170	2126540	318	50	193	75	364
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.49	0.47	0.52	231	1615062	273	41	169	63	265
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.46	0.43	0.49	213	1665792	286	43	177	66	282
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.74	0.66	0.82	304	1116392	101	11	58	32	154
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.70	0.63	0.79	279	1094105	117	6	70	41	166
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.73	0.65	0.82	294	1119399	104	6	57	41	158
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.74	0.66	0.82	294	1098545	110	6	58	46	152
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.45	0.42	0.48	201	1636722	295	39	183	73	280
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.68	0.59	0.78	262	1215683	119	6	69	44	184
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.63	0.55	0.72	223	945690	133	6	81	46	181
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.63	0.55	0.73	212	1201733	150	4	76	70	172
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.71	0.63	0.80	280	1137437	111	7	62	42	167
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.63	0.55	0.72	216	1152623	164	8	74	82	178
CRW_00800	SSU_rRNA_eukarya links to Rfam database...	0.34	0.29	0.39	137	1401627	256	36	175	45	333
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.67	0.59	0.76	279	1117895	114	13	73	28	191
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.72	0.65	0.80	301	1135902	107	11	64	32	163
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.47	0.44	0.50	221	1606085	276	37	185	54	282
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.49	0.46	0.53	231	1593565	264	35	174	55	275
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.73	0.68	0.78	294	977526	128	10	71	47	140
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.66	0.56	0.77	278	1073486	114	9	72	33	217
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.63	0.52	0.77	280	1500414	135	2	82	51	255
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.61	0.49	0.76	269	1471116	131	6	79	46	278
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.57	0.47	0.69	263	1606145	154	8	112	34	299
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.66	0.55	0.80	299	1433595	117	1	76	40	241
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.66	0.56	0.79	296	1204752	112	8	72	32	231
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.69	0.59	0.80	290	1117898	113	9	63	41	201

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Performance of Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	14717
Total TN	79084976
Total FP	14699
Total FP CONTRA	1711
Total FP INCONS	10923
Total FP COMP	2065
Total FN	15363

Total Scores
MCC	0.513
Average MCC ± 95% Confidence Intervals	0.512 ± 0.027
Sensitivity	0.489
Positive Predictive Value	0.538
Nr of predictions	64

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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_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_00306	SSU_rRNA_eukarya links to Rfam database...	0.28	0.28	0.29	129	1445402	388	63	256	69	333
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.33	0.33	0.33	157	1579284	361	57	255	49	325
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.44	0.41	0.46	205	1611467	295	42	196	57	291
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.43	0.42	0.44	223	2126443	372	38	249	85	311
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.39	0.36	0.42	181	1615070	306	41	211	54	315
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.36	0.37	0.36	181	1665721	382	54	269	59	314
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.70	0.68	0.73	312	1116336	148	19	98	31	146
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_00759	SSU_rRNA_eukarya links to Rfam database...	0.31	0.30	0.32	145	1636697	372	51	252	69	336
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.38	0.32	0.44	144	1215694	231	27	155	49	302
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.40	0.37	0.44	148	945666	215	18	168	29	256
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.52	0.45	0.59	174	1201730	163	16	105	42	210
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.48	0.44	0.53	196	1137416	209	14	160	35	251
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.35	0.33	0.38	131	1152575	263	22	193	48	263
CRW_00800	SSU_rRNA_eukarya links to Rfam database...	0.57	0.54	0.60	253	1401550	230	21	151	58	217
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_01153	SSU_rRNA_eukarya links to Rfam database...	0.39	0.39	0.40	194	1606043	347	52	239	56	309
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.45	0.44	0.47	221	1593534	302	49	201	52	285
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.46	0.44	0.48	189	977509	217	30	173	14	245
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.53	0.50	0.56	246	1073403	229	19	177	33	249
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.50	0.49	0.52	264	1500266	296	25	223	48	271
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.46	0.43	0.49	236	1470988	271	34	212	25	311
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.55	0.54	0.56	301	1605989	279	31	207	41	261
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_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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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 MXScarna(seed) - scored higher in this pairwise comparison

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

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

Performance of Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

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