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	CentroidAlifold(seed)		PETfold_pre2.0(20)
MCC	0.799	>	0.786
Average MCC ± 95% Confidence Intervals	0.793 ± 0.033	>	0.787 ± 0.026
Sensitivity	0.708	<	0.759
Positive Predictive Value	0.901	>	0.814
Total TP	19446	<	20829
Total TN	72152542	>	72148550
Total FP	3058	<	6640
Total FP CONTRA	409	<	855
Total FP INCONS	1734	<	3897
Total FP COMP	915	<	1888
Total FN	8007	>	6624
P-value	3.56938820447e-08

^top

Performance plots

Comparison of performance of CentroidAlifold(seed) and PETfold_pre2.0(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 CentroidAlifold(seed) and PETfold_pre2.0(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 CentroidAlifold(seed) and PETfold_pre2.0(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(seed) and PETfold_pre2.0(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 CentroidAlifold(seed) and PETfold_pre2.0(20)).

^top

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

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

Total Base Pair Counts
Total TP	19446
Total TN	72152542
Total FP	3058
Total FP CONTRA	409
Total FP INCONS	1734
Total FP COMP	915
Total FN	8007

Total Scores
MCC	0.799
Average MCC ± 95% Confidence Intervals	0.793 ± 0.033
Sensitivity	0.708
Positive Predictive Value	0.901
Nr of predictions	58

^top

2. Individual counts for CentroidAlifold(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...	0.90	0.86	0.95	393	1085187	55	6	15	34	65
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.90	368	1141906	52	10	32	10	106
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.93	385	1170801	38	9	20	9	85
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.93	374	1107413	39	9	20	10	82
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.92	372	1172342	41	9	23	9	101
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.92	381	1181541	41	9	22	10	95
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.93	375	1108900	39	9	21	9	82
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.87	0.80	0.93	373	1178481	41	4	22	15	92
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.92	379	1135867	41	9	23	9	84
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.93	381	1201614	41	9	21	11	95
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.93	372	1152519	39	9	21	9	94
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.93	376	1180010	40	9	21	10	95
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.94	374	1190796	41	4	22	15	94
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.82	0.76	0.88	340	1082268	59	9	39	11	105
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.84	0.78	0.91	368	1178477	47	9	26	12	105
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.93	383	1207823	39	9	20	10	92
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.93	381	1198515	40	9	21	10	97
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.93	372	1105927	39	9	20	10	81
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.85	0.78	0.92	379	1218731	41	9	22	10	105
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.92	382	1198513	40	9	22	9	96
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.93	374	1192336	40	9	21	10	94
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.93	373	1111883	39	9	21	9	82
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.90	358	1122354	48	8	31	9	104
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.86	0.81	0.92	361	1085207	41	8	25	8	85
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.92	371	1114869	40	9	22	9	86
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.90	363	1110392	50	13	27	10	90
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.83	0.77	0.90	347	1129872	48	8	29	11	103
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.92	371	1180013	46	9	23	14	93
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.90	357	1117863	52	9	31	12	96
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.86	0.79	0.92	368	1144943	39	9	21	9	96
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.90	360	1131361	50	9	30	11	96
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	361	1117862	46	11	26	9	97
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.83	0.77	0.90	367	1189245	50	10	31	9	109
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.53	0.37	0.77	170	1445629	73	4	47	22	292
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.53	0.37	0.77	177	1579523	74	4	49	21	305
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.54	0.37	0.78	185	1611673	73	4	48	21	311
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.45	0.30	0.69	158	2126723	93	6	66	21	376
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.53	0.37	0.76	182	1615264	78	4	53	21	314
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.52	0.36	0.74	177	1665987	83	5	56	22	318
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.93	374	1116361	39	8	22	9	84
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.93	360	1094074	43	2	24	17	85
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.93	364	1119366	44	2	24	18	88
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.88	0.82	0.94	365	1098513	44	3	22	19	81
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.50	0.35	0.72	168	1636913	92	3	61	28	313
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.80	0.74	0.87	297	945660	69	2	41	26	107
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.92	353	1137401	53	5	27	21	94
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.81	0.74	0.88	291	1152590	94	3	37	54	103
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.82	0.76	0.89	358	1117856	57	12	34	11	112
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.93	377	1135871	39	9	21	9	87
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.48	0.33	0.70	167	1606289	89	4	68	17	336
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.52	0.35	0.77	179	1593773	71	4	49	18	327
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.81	0.72	0.92	356	1073456	57	6	27	24	139
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.78	0.66	0.92	354	1500393	66	5	26	35	181
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.75	0.63	0.90	344	1471089	68	3	34	31	203
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.78	0.65	0.92	368	1606129	52	6	25	21	194
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.79	0.68	0.93	367	1433576	53	2	26	25	173
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.80	0.70	0.92	368	1204728	49	8	24	17	159
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.80	0.71	0.90	348	1117874	63	6	32	25	143

^top

Performance of PETfold_pre2.0(20) - scored lower in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(20)

Total Base Pair Counts
Total TP	20829
Total TN	72148550
Total FP	6640
Total FP CONTRA	855
Total FP INCONS	3897
Total FP COMP	1888
Total FN	6624

Total Scores
MCC	0.786
Average MCC ± 95% Confidence Intervals	0.787 ± 0.026
Sensitivity	0.759
Positive Predictive Value	0.814
Nr of predictions	58

^top

2. Individual counts for PETfold_pre2.0(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...	0.89	0.88	0.90	404	1085151	82	10	36	36	54
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.82	0.79	0.85	374	1141875	86	17	50	19	100
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.84	0.83	0.84	390	1170753	91	18	54	19	80
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.84	0.84	0.84	381	1107361	95	17	57	21	75
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.84	0.82	0.85	390	1172289	85	17	50	18	83
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.84	0.82	0.86	390	1181501	85	16	46	23	86
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.84	0.84	0.84	383	1108851	87	16	55	16	74
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.85	0.83	0.87	388	1178436	81	12	44	25	77
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.85	0.84	0.86	388	1135827	85	15	48	22	75
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.83	0.81	0.85	387	1201568	90	18	52	20	89
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.83	0.82	0.85	381	1152473	90	16	51	23	85
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.83	0.81	0.85	381	1179968	89	17	50	22	90
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.85	0.83	0.86	387	1190748	90	11	50	29	81
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.80	0.80	0.81	354	1082220	107	18	64	25	91
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.82	0.81	0.84	382	1178424	101	17	57	27	91
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.83	0.81	0.85	387	1207780	91	16	52	23	88
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.85	0.82	0.87	394	1198472	81	16	44	21	84
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.87	0.86	0.87	390	1105881	79	17	40	22	63
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.84	0.82	0.87	396	1218684	87	15	46	26	88
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.83	0.80	0.85	382	1198478	88	15	51	22	96
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.83	0.81	0.85	379	1192296	87	16	49	22	89
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.86	0.86	0.86	390	1111833	85	15	48	22	65
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.82	0.81	0.84	375	1122302	98	14	60	24	87
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.84	0.84	0.84	375	1085156	94	14	56	24	71
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.86	0.86	0.87	391	1114821	86	15	44	27	66
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.84	0.84	0.85	379	1110348	89	16	52	21	74
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.84	0.82	0.86	371	1129827	85	12	46	27	79
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.82	0.81	0.84	377	1179965	98	18	56	24	87
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.85	0.85	0.86	384	1117811	93	15	50	28	69
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.84	0.82	0.85	381	1144895	89	14	51	24	83
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.84	0.82	0.85	376	1131317	94	16	51	27	80
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.84	0.83	0.86	380	1117816	91	17	47	27	78
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.83	0.81	0.85	386	1189199	95	13	55	27	90
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.60	0.57	0.63	263	1445430	208	26	131	51	199
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.60	0.56	0.64	269	1579331	210	25	128	57	213
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.58	0.55	0.60	275	1611455	232	17	163	52	221
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.58	0.52	0.65	277	2126526	213	25	125	63	257
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.58	0.54	0.61	269	1615064	222	21	149	52	227
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.57	0.53	0.62	263	1665801	210	25	136	49	232
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.85	0.85	0.85	388	1116310	90	13	54	23	70
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.84	0.82	0.86	367	1094034	98	8	51	39	78
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.87	0.84	0.89	381	1119329	87	4	42	41	71
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.85	0.84	0.86	373	1098469	103	7	54	42	73
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.56	0.53	0.59	254	1636715	232	18	158	56	227
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.78	0.76	0.80	306	945618	127	7	69	51	98
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.82	0.80	0.85	357	1137365	108	8	56	44	90
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.79	0.76	0.82	301	1152552	149	5	63	81	93
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.80	0.78	0.82	366	1117816	101	14	64	23	104
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.85	0.84	0.85	389	1135822	85	16	51	18	75
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.59	0.56	0.63	283	1606076	220	25	144	51	220
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.52	0.48	0.56	245	1593566	240	31	163	46	261
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.78	0.72	0.84	355	1073423	101	6	61	34	140
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.75	0.68	0.84	363	1500344	118	10	61	47	172
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.74	0.65	0.83	357	1471042	115	5	66	44	190
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.75	0.66	0.85	373	1606088	99	8	59	32	189
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.75	0.68	0.84	366	1433533	107	4	68	35	174
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.78	0.72	0.85	378	1204681	101	9	60	32	149
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.78	0.73	0.84	358	1117834	110	9	59	42	133

^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 CentroidAlifold(seed) - scored higher in this pairwise comparison

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

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

Performance of PETfold_pre2.0(20) - scored lower in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(20)

2. Individual counts for PETfold_pre2.0(20) [ download as .csv ]