CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ContextFold		RSpredict(20)
MCC	0.725	>	0.012
Average MCC ± 95% Confidence Intervals	0.730 ± 0.051	>	0.013 ± 0.003
Sensitivity	0.688	>	0.012
Positive Predictive Value	0.765	>	0.014
Total TP	25438	>	436
Total TN	104337206	<	104338716
Total FP	9384	<	32060
Total FP CONTRA	1325	<	4727
Total FP INCONS	6497	<	26587
Total FP COMP	1562	>	746
Total FN	11526	<	36528
P-value	3.56938820447e-08

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Performance plots

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

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Performance of ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP	25438
Total TN	104337206
Total FP	9384
Total FP CONTRA	1325
Total FP INCONS	6497
Total FP COMP	1562
Total FN	11526

Total Scores
MCC	0.725
Average MCC ± 95% Confidence Intervals	0.730 ± 0.051
Sensitivity	0.688
Positive Predictive Value	0.765
Nr of predictions	77

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2. Individual counts for ContextFold [ 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...	0.95	0.92	0.98	423	1085170	15	3	5	7	35
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.91	0.89	0.93	421	1141864	43	16	15	12	53
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.94	0.90	0.98	421	1170787	8	3	4	1	49
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.94	0.90	0.97	412	1107393	12	2	9	1	44
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.91	0.88	0.95	416	1172309	22	2	19	1	57
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.94	0.90	0.97	429	1181511	14	7	6	1	47
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.95	0.92	0.99	421	1108878	11	2	4	5	36
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.96	0.92	0.99	430	1178445	8	0	5	3	35
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.93	0.90	0.97	415	1135850	16	2	11	3	48
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.93	0.89	0.97	426	1201584	22	4	11	7	50
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.85	0.81	0.90	376	1152502	48	6	37	5	90
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.91	0.87	0.95	412	1179984	23	8	12	3	59
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.95	0.91	0.99	427	1190763	11	0	6	5	41
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.78	0.71	0.85	318	1082280	60	6	52	2	127
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.92	0.88	0.97	417	1178448	25	2	13	10	56
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.94	0.89	1.00	424	1207810	4	1	0	3	51
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.94	0.90	0.97	431	1198483	18	4	8	6	47
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.93	0.89	0.97	404	1105911	13	2	11	0	49
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.92	0.89	0.96	433	1218688	25	3	17	5	51
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.94	0.91	0.98	435	1198481	12	4	6	2	43
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.91	376	1192327	51	4	33	14	92
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.91	0.86	0.95	391	1111876	31	0	19	12	64
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.92	0.88	0.98	405	1122336	12	2	8	2	57
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.91	0.86	0.97	383	1085207	14	1	10	3	63
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.94	0.90	0.98	412	1114849	15	3	7	5	45
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.83	0.79	0.87	359	1110384	57	9	43	5	94
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.77	0.70	0.84	316	1129880	68	9	51	8	134
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.89	0.84	0.94	389	1180004	36	4	19	13	75
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.92	0.88	0.95	398	1117843	21	4	15	2	55
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.92	0.87	0.96	405	1144919	21	2	15	4	59
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.89	365	1131352	48	0	43	5	91
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.95	0.91	0.99	416	1117839	7	2	3	2	42
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.90	382	1189229	44	4	38	2	94
CRW_00298	SSU_rRNA_eukarya links to Rfam database...	0.38	0.35	0.41	173	1620475	275	37	215	23	321
CRW_00301	SSU_rRNA_eukarya links to Rfam database...	0.51	0.47	0.55	245	1762058	245	26	174	45	274
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.37	0.36	0.37	168	1445399	304	63	220	21	294
CRW_00310	SSU_rRNA_eukarya links to Rfam database...	0.49	0.47	0.52	243	1805487	271	31	189	51	278
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.58	0.54	0.63	271	1627677	194	30	132	32	231
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.47	0.45	0.49	232	1988538	308	45	200	63	285
CRW_00332	SSU_rRNA_eukarya links to Rfam database...	0.50	0.46	0.54	218	1769618	245	34	151	60	259
CRW_00333	SSU_rRNA_eukarya links to Rfam database...	0.36	0.33	0.40	171	1892055	315	40	219	56	343
CRW_00345	SSU_rRNA_eukarya links to Rfam database...	0.39	0.38	0.41	187	1586412	289	48	224	17	311
CRW_00346	SSU_rRNA_eukarya links to Rfam database...	0.36	0.34	0.38	172	1584635	308	55	228	25	329
CRW_00348	SSU_rRNA_eukarya links to Rfam database...	0.46	0.44	0.49	219	1615055	262	39	190	33	284
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.46	0.45	0.47	227	1674887	268	53	198	17	280
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.45	0.42	0.48	202	1579334	251	36	181	34	280
CRW_00370	SSU_rRNA_eukarya links to Rfam database...	0.37	0.35	0.39	176	1640316	302	35	239	28	330
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.56	0.53	0.58	263	1611460	230	33	154	43	233
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.47	0.45	0.49	225	1625846	264	44	191	29	273
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.62	0.59	0.65	314	2126472	237	36	131	70	220
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.39	0.38	0.39	197	1750754	338	55	250	33	318
CRW_00403	SSU_rRNA_eukarya links to Rfam database...	0.51	0.48	0.55	222	1606122	262	30	154	78	242
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.55	0.52	0.59	257	1615067	222	34	145	43	239
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.43	0.41	0.44	205	1665761	293	45	214	34	290
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.95	0.92	0.98	421	1116336	10	3	5	2	37
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.90	350	1094071	49	3	36	10	95
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	358	1119364	45	3	31	11	94
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.92	0.88	0.96	393	1098492	32	6	12	14	53
CRW_00598	SSU_rRNA_eukarya links to Rfam database...	0.31	0.29	0.34	144	1665799	323	40	242	41	347
CRW_00758	SSU_rRNA_eukarya links to Rfam database...	0.46	0.45	0.48	217	1640313	290	20	216	54	266
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.40	0.38	0.42	181	1636714	284	45	205	34	300
CRW_00760	SSU_rRNA_eukarya links to Rfam database...	0.41	0.39	0.43	189	1638513	310	51	202	57	297
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.71	0.65	0.79	262	945667	95	9	62	24	142
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.91	357	1137392	54	3	34	17	90
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.65	0.59	0.71	232	1152596	140	14	79	47	162
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.93	0.90	0.96	425	1117816	31	1	18	12	45
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.92	0.90	0.95	419	1135835	28	6	18	4	45
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.41	0.40	0.43	199	1606068	288	37	224	27	304
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.50	0.47	0.53	237	1593555	238	35	178	25	269
CRW_01300	SSU_rRNA_eukarya links to Rfam database...	0.38	0.36	0.40	185	1693252	309	52	231	26	330
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.87	0.79	0.96	392	1073435	37	4	14	19	103
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.90	0.85	0.95	455	1500298	52	7	18	27	80
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.85	0.78	0.93	426	1471011	64	4	29	31	121
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.86	0.81	0.91	455	1606027	68	3	43	22	107
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.90	0.85	0.96	459	1433493	36	3	16	17	81
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.88	0.80	0.97	422	1204693	33	2	11	20	105
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.86	0.78	0.94	385	1117852	50	4	19	27	106

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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	436
Total TN	104338716
Total FP	32060
Total FP CONTRA	4727
Total FP INCONS	26587
Total FP COMP	746
Total FN	36528

Total Scores
MCC	0.012
Average MCC ± 95% Confidence Intervals	0.013 ± 0.003
Sensitivity	0.012
Positive Predictive Value	0.014
Nr of predictions	77

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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...	0.00	0.00	0.00	0	1085139	462	69	393	0	458
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1141928	389	59	329	1	474
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1170785	432	69	361	2	470
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.03	0.03	0.03	14	1107398	407	51	353	3	442
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1172337	401	54	346	1	464
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1181530	414	57	357	0	467
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1108900	397	50	346	1	448
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1178457	425	69	354	2	465
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	10	1135850	420	52	366	2	453
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1201601	424	53	371	0	476
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	1	1152501	423	55	364	4	465
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1179985	433	63	368	2	471
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1190754	442	64	378	0	468
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.01	0.01	0.01	3	1082257	404	52	344	8	442
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.01	0.01	0.01	4	1178459	419	57	360	2	469
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1207806	431	77	352	2	475
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1198500	417	63	354	0	469
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.03	10	1105929	391	75	314	2	443
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1218696	448	74	371	3	484
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1198499	431	60	367	4	478
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1192334	416	54	352	10	468
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	10	1111874	406	58	344	4	445
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.03	0.03	0.03	12	1122350	389	52	337	0	450
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1085210	383	50	332	1	437
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1114870	392	54	338	0	448
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.03	0.03	0.03	12	1110392	394	69	322	3	441
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.04	0.04	0.05	19	1129855	384	58	324	2	431
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1180000	419	62	354	3	464
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1117843	408	79	329	0	444
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	10	1144926	405	59	346	0	454
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	10	1131353	400	72	325	3	446
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1117861	393	58	332	3	449
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.09	0.09	0.10	43	1189225	390	55	330	5	433
CRW_00298	SSU_rRNA_eukarya links to Rfam database...	0.01	0.01	0.01	3	1620508	410	63	326	21	491
CRW_00301	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1762034	472	82	379	11	511
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1445474	405	54	322	29	462
CRW_00310	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1805520	442	63	359	20	513
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1627675	437	70	357	10	494
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1988575	477	82	350	45	509
CRW_00332	SSU_rRNA_eukarya links to Rfam database...	0.01	0.01	0.01	3	1769654	389	59	305	25	474
CRW_00333	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	1	1892051	454	80	353	21	513
CRW_00345	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1586488	384	57	318	9	490
CRW_00346	SSU_rRNA_eukarya links to Rfam database...	0.01	0.01	0.01	4	1584683	432	63	340	29	497
CRW_00348	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1615104	410	69	330	11	503
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1674979	406	62	324	20	507
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.01	0.01	0.01	4	1579393	371	66	290	15	478
CRW_00370	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	10	1640309	469	52	395	22	496
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1611495	424	63	344	17	488
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1625926	390	51	321	18	490
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	2126541	465	66	346	53	534
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1750835	427	65	348	14	507
CRW_00403	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1606168	385	68	292	25	464
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...	0.01	0.01	0.01	3	1665773	466	78	371	17	492
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1116356	402	42	358	2	449
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1094068	388	55	328	5	436
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	10	1119344	403	68	334	1	442
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	10	1098502	403	46	345	12	436
CRW_00598	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1665800	449	72	353	24	491
CRW_00758	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1640340	444	79	347	18	483
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	9	1636732	429	64	340	25	472
CRW_00760	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1638553	425	77	325	23	486
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.01	2	945654	349	60	284	5	402
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1137394	389	58	325	6	438
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.04	0.04	0.04	16	1152547	382	70	288	24	378
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1117851	401	56	344	1	461
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1135858	413	68	343	2	455
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1606093	451	64	371	16	503
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.02	0.01	0.02	7	1593610	403	61	327	15	499
CRW_01300	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1693285	445	62	373	10	515
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	10	1073431	406	37	367	2	485
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1500347	438	69	362	7	535
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1471042	432	49	379	4	547
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1606098	437	45	385	7	562
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.01	0.01	0.01	3	1433548	430	47	373	10	537
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1204692	440	41	395	4	527
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	2	1117847	415	47	364	4	489

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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 ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

2. Individual counts for ContextFold [ 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 ]