CompaRNA - on-line benchmarks of RNA structure prediction methods

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Overview

Metric	MXScarna(seed)		IPknot
MCC	0.659	>	0.581
Average MCC ± 95% Confidence Intervals	0.662 ± 0.026	>	0.577 ± 0.033
Sensitivity	0.589	>	0.505
Positive Predictive Value	0.738	>	0.670
Total TP	17728	>	15195
Total TN	79088306	<	79089635
Total FP	8922	>	8884
Total FP CONTRA	930	<	1175
Total FP INCONS	5363	<	6322
Total FP COMP	2629	>	1387
Total FN	12352	<	14885
P-value	3.56938820447e-08

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Performance plots

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

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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 IPknot - scored lower in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	15195
Total TN	79089635
Total FP	8884
Total FP CONTRA	1175
Total FP INCONS	6322
Total FP COMP	1387
Total FN	14885

Total Scores
MCC	0.581
Average MCC ± 95% Confidence Intervals	0.577 ± 0.033
Sensitivity	0.505
Positive Predictive Value	0.670
Nr of predictions	64

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2. Individual counts for IPknot [ 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	0.77	0.89	352	1085204	78	4	41	33	106
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.78	0.76	0.79	360	1141862	121	19	75	27	114
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.72	0.63	0.83	297	1170856	75	6	56	13	173
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.58	0.50	0.66	229	1107469	137	16	102	19	227
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.71	0.61	0.83	287	1172399	74	4	56	14	186
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.66	0.60	0.72	287	1181556	121	23	87	11	189
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.59	0.52	0.66	236	1108950	134	23	96	15	221
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.55	0.50	0.60	231	1178495	170	17	137	16	234
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.76	0.68	0.83	317	1135898	79	6	57	16	146
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.70	0.64	0.77	307	1201626	111	11	81	19	169
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.58	0.50	0.68	231	1152582	123	17	91	15	235
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.54	0.48	0.62	225	1180051	148	20	120	8	246
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.61	0.53	0.70	249	1190838	118	6	103	9	219
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.37	0.34	0.40	150	1082284	231	30	192	9	295
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.59	0.53	0.65	252	1178495	145	17	116	12	221
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.61	0.55	0.67	261	1207844	146	17	113	16	214
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.73	0.63	0.85	302	1198569	73	7	48	18	176
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.62	0.53	0.74	239	1106005	96	13	71	12	214
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.76	0.72	0.81	347	1218713	108	15	66	27	137
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.57	0.52	0.63	250	1198526	164	23	127	14	228
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.56	0.44	0.71	207	1192448	104	18	67	19	261
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.66	0.55	0.79	250	1111971	79	11	54	14	205
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.56	0.47	0.66	216	1122424	126	25	86	15	246
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.52	0.47	0.58	208	1085244	163	20	129	14	238
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.76	0.69	0.83	314	1114894	79	11	52	16	143
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.53	0.43	0.66	194	1110503	106	22	76	8	259
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.60	0.48	0.74	218	1129962	95	5	71	19	232
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.66	0.58	0.76	270	1180060	100	16	70	14	194
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.67	0.58	0.77	265	1117916	90	11	68	11	188
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.65	0.59	0.72	276	1144958	123	17	90	16	188
CRW_00283	SSU_rRNA_bacteria links to Rfam database...	0.42	0.31	0.56	136	1015781	124	17	91	16	296
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.55	0.42	0.71	193	1131487	92	13	67	12	263
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.79	0.71	0.88	327	1117890	60	13	30	17	131
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.64	0.56	0.73	268	1189284	121	17	84	20	208
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.41	0.35	0.48	160	1123920	187	28	142	17	301
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.28	0.24	0.34	109	1445531	252	37	173	42	353
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.37	0.32	0.42	153	1579390	248	42	168	38	329
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.49	0.41	0.59	203	1611565	179	27	115	37	293
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.49	0.40	0.59	214	2126590	218	30	119	69	320
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.40	0.34	0.46	170	1615137	238	31	165	42	326
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.41	0.33	0.51	163	1665906	188	30	126	32	332
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.81	0.75	0.88	344	1116375	69	10	36	23	114
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.44	0.37	0.53	164	1094152	163	21	123	19	281
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.53	0.48	0.59	217	1119386	165	27	126	12	235
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.70	0.63	0.77	282	1098536	110	15	70	25	164
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.28	0.24	0.33	116	1636796	279	54	179	46	365
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.48	0.34	0.67	153	1215790	109	10	67	32	293
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.44	0.34	0.57	136	945760	126	16	88	22	268
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.42	0.29	0.60	111	1201840	104	12	62	30	273
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.55	0.46	0.66	206	1137473	121	11	96	14	241
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.36	0.26	0.50	102	1152715	143	20	84	39	292
CRW_00800	SSU_rRNA_eukarya links to Rfam database...	0.62	0.51	0.75	240	1401657	117	12	66	39	230
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.68	0.63	0.73	295	1117857	132	9	99	24	175
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.68	0.62	0.75	289	1135893	113	17	79	17	175
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.37	0.35	0.40	174	1606096	291	43	215	33	329
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.45	0.41	0.50	207	1593595	240	34	169	37	299
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.50	0.42	0.59	182	977595	134	16	108	10	252
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.64	0.57	0.72	282	1073454	132	13	96	23	213
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.67	0.62	0.73	331	1500326	158	17	104	37	204
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.55	0.46	0.66	252	1471087	150	21	110	19	295
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.62	0.57	0.67	319	1606055	171	20	134	17	243
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.69	0.63	0.76	342	1433519	132	10	100	22	198
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.56	0.48	0.66	252	1204748	138	22	106	10	275
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.61	0.56	0.67	276	1117847	163	10	127	26	215

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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 IPknot - scored lower in this pairwise comparison

1. Total counts & total scores for IPknot

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