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)		RSpredict(20)
MCC	0.665	>	0.591
Average MCC ± 95% Confidence Intervals	0.668 ± 0.027	>	0.594 ± 0.057
Sensitivity	0.595	>	0.530
Positive Predictive Value	0.743	>	0.659
Total TP	16336	>	14560
Total TN	72152147	>	72152050
Total FP	8016	<	9115
Total FP CONTRA	849	<	1285
Total FP INCONS	4799	<	6236
Total FP COMP	2368	>	1594
Total FN	11117	<	12893
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of MXScarna(seed) and RSpredict(20). 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 RSpredict(20)).
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 RSpredict(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(seed) and RSpredict(20). 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 RSpredict(20)).

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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	16336
Total TN	72152147
Total FP	8016
Total FP CONTRA	849
Total FP INCONS	4799
Total FP COMP	2368
Total FN	11117

Total Scores
MCC	0.665
Average MCC ± 95% Confidence Intervals	0.668 ± 0.027
Sensitivity	0.595
Positive Predictive Value	0.743
Nr of predictions	58

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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_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_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_00772	SSU_rRNA_bacteria links to Rfam database...	0.63	0.55	0.72	223	945690	133	6	81	46	181
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_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
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 RSpredict(20) - scored lower in this pairwise comparison

1. Total counts & total scores for RSpredict(20)

Total Base Pair Counts
Total TP	14560
Total TN	72152050
Total FP	9115
Total FP CONTRA	1285
Total FP INCONS	6236
Total FP COMP	1594
Total FN	12893

Total Scores
MCC	0.591
Average MCC ± 95% Confidence Intervals	0.594 ± 0.057
Sensitivity	0.530
Positive Predictive Value	0.659
Nr of predictions	58

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2. Individual counts for RSpredict(20) [ 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...	0.78	0.76	0.80	349	1085166	117	16	70	31	109
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.60	0.50	0.71	239	1141980	119	16	81	22	235
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.74	0.71	0.78	332	1170788	124	21	74	29	138
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.72	0.68	0.76	308	1107412	121	17	79	25	148
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.73	0.68	0.78	320	1172336	118	19	71	28	153
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.63	0.55	0.72	260	1181590	123	18	85	20	216
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.73	0.69	0.77	314	1108895	119	18	78	23	143
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.73	0.69	0.78	320	1178470	123	16	74	33	145
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.73	0.68	0.79	316	1135876	116	15	71	30	147
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.72	0.67	0.77	320	1201607	124	19	79	26	156
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.73	0.68	0.79	315	1152520	110	20	66	24	151
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.71	0.65	0.77	308	1180015	120	17	76	27	163
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.73	0.68	0.79	317	1190796	115	15	68	32	151
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.68	0.63	0.74	281	1082274	126	20	81	25	164
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.66	0.60	0.74	283	1178495	122	22	80	20	190
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.71	0.67	0.76	316	1207819	125	23	77	25	159
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.72	0.67	0.77	319	1198513	119	20	74	25	159
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.70	0.63	0.78	285	1105963	105	14	66	25	168
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.71	0.67	0.76	322	1218719	127	19	81	27	162
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.72	0.66	0.78	317	1198517	119	19	73	27	161
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.71	0.62	0.81	292	1192380	91	18	50	23	176
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.68	0.60	0.77	272	1111934	101	13	67	21	183
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.70	0.65	0.75	301	1122349	125	21	80	24	161
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.67	0.60	0.76	266	1085250	106	16	69	21	180
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.73	0.69	0.77	315	1114864	116	18	74	24	142
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.62	0.54	0.71	244	1110451	120	17	83	20	209
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.60	0.51	0.71	231	1129930	115	14	81	20	219
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.71	0.66	0.75	308	1180005	131	20	83	28	156
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.71	0.66	0.75	300	1117861	125	19	80	26	153
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.72	0.67	0.77	311	1144937	123	15	78	30	153
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.71	0.66	0.77	301	1131370	113	18	71	24	155
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.64	0.55	0.73	254	1117913	115	15	78	22	204
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.70	0.66	0.76	312	1189241	126	19	81	26	164
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.37	0.34	0.39	158	1445446	293	34	212	47	304
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.01	0.01	0.01	4	1579393	371	66	290	15	478
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1611495	424	63	344	17	488
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	2126541	465	66	346	53	534
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1615135	382	74	294	14	496
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.33	0.31	0.36	152	1665808	305	45	220	40	343
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.64	0.56	0.73	258	1116413	115	15	79	21	200
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.64	0.55	0.75	244	1094136	105	9	71	25	201
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.63	0.55	0.73	249	1119415	115	6	86	23	203
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.70	0.63	0.76	283	1098533	118	13	74	31	163
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	9	1636732	429	64	340	25	472
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.59	0.49	0.71	196	945723	109	10	71	28	208
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.65	0.57	0.75	254	1137446	113	13	73	27	193
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.63	0.53	0.75	209	1152644	114	10	58	46	185
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.61	0.51	0.72	241	1117925	111	14	80	17	229
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.73	0.69	0.77	319	1135862	125	18	79	28	145
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.35	0.31	0.40	155	1606145	262	44	184	34	348
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.02	0.01	0.02	7	1593610	403	61	327	15	499
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.67	0.60	0.75	297	1073447	132	13	88	31	198
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.62	0.50	0.76	266	1500430	124	10	72	42	269
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.62	0.49	0.77	268	1471123	123	8	71	44	279
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.63	0.49	0.80	278	1606180	104	12	58	34	284
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.61	0.50	0.75	270	1433609	124	8	84	32	270
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.64	0.54	0.76	282	1204758	129	8	80	41	245
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.69	0.62	0.77	305	1117865	121	14	76	31	186

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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 RSpredict(20) - scored lower in this pairwise comparison

1. Total counts & total scores for RSpredict(20)

2. Individual counts for RSpredict(20) [ download as .csv ]