CompaRNA - on-line benchmarks of RNA structure prediction methods

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Overview

Metric	MXScarna(seed)		MaxExpect
MCC	0.659	>	0.440
Average MCC ± 95% Confidence Intervals	0.662 ± 0.026	>	0.439 ± 0.029
Sensitivity	0.589	>	0.428
Positive Predictive Value	0.738	>	0.454
Total TP	17728	>	12861
Total TN	79088306	>	79083988
Total FP	8922	<	17193
Total FP CONTRA	930	<	2098
Total FP INCONS	5363	<	13380
Total FP COMP	2629	>	1715
Total FN	12352	<	17219
P-value	3.56938820447e-08

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Performance plots

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

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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 MaxExpect - scored lower in this pairwise comparison

1. Total counts & total scores for MaxExpect

Total Base Pair Counts
Total TP	12861
Total TN	79083988
Total FP	17193
Total FP CONTRA	2098
Total FP INCONS	13380
Total FP COMP	1715
Total FN	17219

Total Scores
MCC	0.440
Average MCC ± 95% Confidence Intervals	0.439 ± 0.029
Sensitivity	0.428
Positive Predictive Value	0.454
Nr of predictions	64

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2. Individual counts for MaxExpect [ 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...	0.71	0.70	0.71	320	1085152	169	17	112	40	138
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.66	0.65	0.66	310	1141844	191	28	134	29	164
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.52	0.48	0.57	226	1170816	189	20	153	16	244
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.43	0.42	0.44	192	1107377	261	23	224	14	264
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.51	0.49	0.54	232	1172316	212	16	182	14	241
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.44	0.43	0.45	203	1181497	266	35	218	13	273
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.44	0.43	0.45	197	1108869	251	32	207	12	260
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.49	0.47	0.52	220	1178453	229	21	186	22	245
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.43	0.42	0.44	193	1135835	265	20	230	15	270
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.54	0.53	0.55	254	1201566	230	30	175	25	222
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.44	0.43	0.46	202	1152479	257	24	216	17	264
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.58	0.55	0.60	259	1179986	190	37	134	19	212
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.43	0.41	0.46	192	1190777	241	18	209	14	276
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.26	0.26	0.27	115	1082230	324	28	283	13	330
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.48	0.47	0.50	221	1178440	239	26	193	20	252
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.50	0.49	0.51	233	1207782	238	32	188	18	242
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.58	0.55	0.60	263	1198489	199	15	159	25	215
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.42	0.41	0.43	186	1105895	262	25	222	15	267
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.51	0.51	0.51	248	1218656	263	29	208	26	236
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.51	0.50	0.51	241	1198458	244	44	183	17	237
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.40	0.39	0.41	182	1192293	285	38	227	20	286
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.54	0.54	0.55	244	1111842	223	23	177	23	211
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.33	0.32	0.34	146	1122327	292	34	244	14	316
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.42	0.40	0.45	180	1085197	237	27	197	13	266
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.61	0.60	0.62	273	1114831	186	26	141	19	184
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.35	0.33	0.37	148	1110390	267	37	220	10	305
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.39	0.36	0.42	160	1129876	240	22	198	20	290
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.54	0.53	0.56	244	1179977	213	26	169	18	220
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.36	0.35	0.37	157	1117836	279	37	230	12	296
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.59	0.58	0.60	270	1144891	201	25	155	21	194
CRW_00283	SSU_rRNA_bacteria links to Rfam database...	0.35	0.34	0.36	146	1015622	282	41	216	25	286
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.38	0.35	0.41	159	1131368	249	21	212	16	297
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.56	0.54	0.58	246	1117835	199	26	153	20	212
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.48	0.46	0.50	218	1189213	245	32	190	23	258
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.35	0.33	0.37	150	1123843	269	39	218	12	311
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.18	0.19	0.18	86	1445370	462	62	332	68	376
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.27	0.28	0.26	134	1579236	421	78	305	38	348
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.40	0.39	0.42	192	1611452	316	45	221	50	304
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.44	0.44	0.43	234	2126414	384	57	248	79	300
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.33	0.33	0.34	163	1615021	361	68	251	42	333
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.30	0.31	0.30	153	1665712	421	60	300	61	342
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.61	0.60	0.62	273	1116325	188	25	142	21	185
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.32	0.31	0.34	136	1094057	285	28	239	18	309
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.40	0.37	0.43	169	1119363	246	23	201	22	283
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.44	0.43	0.44	194	1098463	264	36	210	18	252
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.31	0.31	0.30	151	1636649	407	59	286	62	330
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.20	0.19	0.21	86	1215616	348	38	280	30	360
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.22	0.21	0.23	85	945632	297	29	254	14	319
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.29	0.29	0.29	112	1201643	316	45	225	46	272
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.37	0.37	0.38	165	1137350	293	39	232	22	282
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.35	0.35	0.35	138	1152523	307	34	226	47	256
CRW_00800	SSU_rRNA_eukarya links to Rfam database...	0.55	0.51	0.59	239	1401570	232	20	146	66	231
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.58	0.58	0.59	271	1117802	215	14	173	28	199
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.44	0.42	0.45	197	1135837	260	32	212	16	267
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.30	0.30	0.30	151	1606020	397	56	301	40	352
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.33	0.33	0.34	167	1593511	375	57	270	48	339
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.37	0.35	0.38	154	977498	261	31	218	12	280
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.57	0.52	0.62	259	1073427	187	20	139	28	236
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.58	0.56	0.60	298	1500283	247	21	176	50	237
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.33	0.32	0.35	176	1470965	353	46	283	24	371
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.63	0.60	0.67	337	1606027	197	18	146	33	225
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.57	0.54	0.60	289	1433488	229	24	170	35	251
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.43	0.40	0.46	211	1204672	264	28	217	19	316
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.45	0.43	0.46	211	1117804	273	31	214	28	280

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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 MaxExpect - scored lower in this pairwise comparison

1. Total counts & total scores for MaxExpect

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