CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	MXScarna(seed)		PknotsRG
MCC	0.702	>	0.435
Average MCC ± 95% Confidence Intervals	0.701 ± 0.018	>	0.432 ± 0.035
Sensitivity	0.626	>	0.430
Positive Predictive Value	0.788	>	0.441
Total TP	15021	>	10306
Total TN	59630609	>	59626314
Total FP	5972	<	14139
Total FP CONTRA	540	<	1732
Total FP INCONS	3509	<	11327
Total FP COMP	1923	>	1080
Total FN	8960	<	13675
P-value	3.56938820447e-08

^top

Performance plots

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

^top

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

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

Total Base Pair Counts
Total TP	15021
Total TN	59630609
Total FP	5972
Total FP CONTRA	540
Total FP INCONS	3509
Total FP COMP	1923
Total FN	8960

Total Scores
MCC	0.702
Average MCC ± 95% Confidence Intervals	0.701 ± 0.018
Sensitivity	0.626
Positive Predictive Value	0.788
Nr of predictions	52

^top

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_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_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_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_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

^top

Performance of PknotsRG - scored lower in this pairwise comparison

1. Total counts & total scores for PknotsRG

Total Base Pair Counts
Total TP	10306
Total TN	59626314
Total FP	14139
Total FP CONTRA	1732
Total FP INCONS	11327
Total FP COMP	1080
Total FN	13675

Total Scores
MCC	0.435
Average MCC ± 95% Confidence Intervals	0.432 ± 0.035
Sensitivity	0.430
Positive Predictive Value	0.441
Nr of predictions	52

^top

2. Individual counts for PknotsRG [ 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	0.76	0.79	348	1085160	130	18	75	37	110
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.63	0.63	0.63	300	1141843	196	31	142	23	174
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.45	0.45	0.45	210	1170748	276	27	230	19	260
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.53	0.52	0.54	236	1107378	216	34	168	14	220
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.50	0.49	0.51	233	1172293	234	28	192	14	240
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.43	0.44	0.43	208	1181469	284	32	244	8	268
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.33	0.33	0.34	152	1108852	312	37	264	11	305
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.55	0.55	0.55	255	1178420	227	21	184	22	210
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.64	0.64	0.65	296	1135820	182	22	140	20	167
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.51	0.50	0.52	238	1201566	240	29	192	19	238
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.41	0.41	0.42	190	1152467	282	34	230	18	276
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.51	0.50	0.52	236	1179961	240	37	182	21	235
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.53	0.52	0.54	242	1190746	234	25	183	26	226
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.29	0.29	0.29	128	1082212	325	37	279	9	317
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.42	0.41	0.42	196	1178413	284	31	240	13	277
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.47	0.46	0.47	220	1207767	270	26	222	22	255
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.55	0.54	0.57	260	1198467	221	30	169	22	218
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.35	0.35	0.34	157	1105872	312	45	254	13	296
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.57	0.57	0.58	275	1218668	230	24	174	32	209
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.43	0.43	0.43	205	1198449	287	30	242	15	273
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.45	0.44	0.46	206	1192291	257	41	202	14	262
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.38	0.37	0.39	168	1111857	279	39	222	18	287
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.49	0.48	0.50	220	1122307	239	36	188	15	242
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.51	0.50	0.51	222	1085169	227	31	179	17	224
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.42	0.42	0.43	193	1114817	278	26	235	17	264
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.25	0.25	0.24	113	1110332	354	55	295	4	340
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.41	0.40	0.42	180	1129825	270	35	216	19	270
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.29	0.29	0.30	134	1179968	334	40	274	20	330
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.50	0.50	0.51	226	1117813	234	28	193	13	227
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.30	0.30	0.30	138	1144878	340	40	285	15	326
CRW_00283	SSU_rRNA_bacteria links to Rfam database...	0.28	0.28	0.29	120	1015605	317	42	258	17	312
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.26	0.25	0.26	115	1131320	336	35	290	11	341
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.47	0.47	0.47	214	1117807	257	31	208	18	244
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.45	0.44	0.46	209	1189197	272	34	213	25	267
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.31	0.30	0.32	138	1123818	305	44	250	11	323
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.61	0.60	0.62	273	1116325	194	25	142	27	185
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.22	0.21	0.22	95	1094029	351	37	299	15	350
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.32	0.31	0.33	141	1119330	303	41	244	18	311
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.61	0.60	0.62	267	1098475	190	19	142	29	179
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.20	0.20	0.21	90	1215581	387	50	299	38	356
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.24	0.24	0.25	97	945607	320	41	255	24	307
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.22	0.22	0.22	84	1201649	346	41	251	54	300
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.35	0.35	0.35	156	1137342	304	48	240	16	291
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.24	0.25	0.23	98	1152503	357	51	269	37	296
CRW_00800	SSU_rRNA_eukarya links to Rfam database...	0.52	0.52	0.52	243	1401506	288	31	195	62	227
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.48	0.48	0.49	225	1117798	260	25	212	23	245
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.52	0.52	0.52	239	1135819	238	24	196	18	225
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.34	0.33	0.34	145	977474	293	46	236	11	289
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.50	0.48	0.53	239	1073392	239	21	193	25	256
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.51	0.50	0.52	269	1433453	278	27	222	29	271
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.48	0.45	0.51	239	1204657	247	27	205	15	288
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.47	0.46	0.49	225	1117799	263	23	213	27	266

^top

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 PknotsRG - scored lower in this pairwise comparison

1. Total counts & total scores for PknotsRG

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