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)		MXScarna(seed)
MCC	0.763	>	0.659
Average MCC ± 95% Confidence Intervals	0.761 ± 0.037	>	0.662 ± 0.026
Sensitivity	0.699	>	0.589
Positive Predictive Value	0.833	>	0.738
Total TP	21025	>	17728
Total TN	79087088	<	79088306
Total FP	5185	<	8922
Total FP CONTRA	983	>	930
Total FP INCONS	3231	<	5363
Total FP COMP	971	<	2629
Total FN	9055	<	12352
P-value	3.56938820447e-08

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Performance plots

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

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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	21025
Total TN	79087088
Total FP	5185
Total FP CONTRA	983
Total FP INCONS	3231
Total FP COMP	971
Total FN	9055

Total Scores
MCC	0.763
Average MCC ± 95% Confidence Intervals	0.761 ± 0.037
Sensitivity	0.699
Positive Predictive Value	0.833
Nr of predictions	64

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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_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_00379	SSU_rRNA_eukarya links to Rfam database...	0.40	0.32	0.50	169	2126616	180	32	136	12	365
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 MXScarna(seed) - scored lower 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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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 MXScarna(seed) - scored lower in this pairwise comparison

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

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