CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAalifold(seed)		RSpredict(20)
MCC	0.743	>	0.014
Average MCC ± 95% Confidence Intervals	0.741 ± 0.041	>	0.014 ± 0.004
Sensitivity	0.677	>	0.013
Positive Predictive Value	0.817	>	0.015
Total TP	19947	>	383
Total TN	78830741	>	78829644
Total FP	5352	<	25573
Total FP CONTRA	1039	<	3699
Total FP INCONS	3441	<	21442
Total FP COMP	872	>	432
Total FN	9528	<	29092
P-value	3.56938820447e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	19947
Total TN	78830741
Total FP	5352
Total FP CONTRA	1039
Total FP INCONS	3441
Total FP COMP	872
Total FN	9528

Total Scores
MCC	0.743
Average MCC ± 95% Confidence Intervals	0.741 ± 0.041
Sensitivity	0.677
Positive Predictive Value	0.817
Nr of predictions	62

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2. Individual counts for RNAalifold(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...	0.87	0.84	0.90	385	1085175	58	7	34	17	73
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.82	0.77	0.88	363	1141905	62	14	34	14	111
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.88	372	1170793	59	16	34	9	98
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.84	0.81	0.88	369	1107397	60	16	34	10	87
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.82	0.78	0.88	367	1172327	61	16	36	9	106
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.82	0.77	0.88	367	1181535	61	16	35	10	109
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.85	0.81	0.88	370	1108886	58	15	34	9	87
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.89	368	1178465	61	12	35	14	97
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.83	0.79	0.87	367	1135858	62	16	37	9	96
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.88	369	1201606	61	16	34	11	107
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	368	1152515	47	13	25	9	98
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	372	1180006	46	13	25	8	99
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.88	365	1190782	64	12	37	15	103
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.79	0.76	0.84	336	1082254	76	16	50	10	109
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.82	0.77	0.87	364	1178460	66	16	40	10	109
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.82	0.77	0.87	365	1207815	63	16	39	8	110
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.83	0.77	0.88	369	1198508	59	15	34	10	109
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.84	0.81	0.88	366	1105912	60	16	34	10	87
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.82	0.76	0.88	369	1218720	61	16	36	9	115
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.82	0.77	0.88	369	1198505	61	16	36	9	109
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	369	1192333	48	13	25	10	99
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.84	0.81	0.88	368	1111868	59	15	35	9	87
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.90	359	1122350	51	13	29	9	103
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.84	0.80	0.87	358	1085191	60	16	36	8	88
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.84	0.80	0.88	366	1114854	59	16	35	8	91
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.83	0.79	0.87	359	1110382	64	17	37	10	94
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.88	349	1129861	58	13	33	12	101
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.91	372	1180005	54	13	26	15	92
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.84	0.80	0.89	363	1117851	59	13	33	13	90
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.91	372	1144932	48	13	24	11	92
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.83	0.78	0.89	356	1131358	59	13	33	13	100
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.82	0.78	0.86	356	1117847	66	17	40	9	102
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.80	0.75	0.86	358	1189235	67	16	44	7	118
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.45	0.39	0.52	178	1445508	175	32	132	11	284
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.44	0.37	0.53	184	1627762	174	32	132	10	318
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.44	0.36	0.53	184	1675017	173	32	132	9	323
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.42	0.36	0.51	172	1579413	180	32	136	12	310
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.44	0.36	0.52	181	1611565	175	31	133	11	315
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.44	0.37	0.53	184	1625958	174	32	132	10	314
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.40	0.32	0.50	169	2126616	180	32	136	12	365
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.44	0.35	0.55	182	1750923	164	28	123	13	333
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.45	0.38	0.55	186	1615165	163	28	124	11	310
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.45	0.37	0.54	182	1665890	171	28	125	18	313
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.86	0.82	0.91	377	1116350	49	12	26	11	81
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.86	0.81	0.92	361	1094068	53	6	25	22	84
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.92	366	1119360	52	6	24	22	86
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.87	0.82	0.92	365	1098507	56	8	23	25	81
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.41	0.34	0.49	163	1636811	183	35	136	12	318
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.81	0.75	0.88	302	945656	72	5	37	30	102
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	355	1137395	59	8	28	23	92
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.78	0.73	0.84	288	1152577	109	10	46	53	106
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.82	0.76	0.88	356	1117856	63	14	34	15	114
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.84	0.80	0.88	372	1135856	59	15	35	9	92
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.41	0.34	0.49	172	1606179	193	36	141	16	331
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.43	0.36	0.52	181	1593657	177	34	133	10	325
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.78	0.69	0.87	344	1073448	73	7	46	20	151
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.74	0.64	0.87	342	1500383	85	10	43	32	193
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.73	0.63	0.86	342	1471073	85	8	47	30	205
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.74	0.63	0.87	355	1606120	72	10	43	19	207
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.76	0.66	0.88	355	1433566	72	7	43	22	185
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.77	0.68	0.87	358	1204715	73	7	48	18	169
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.78	0.70	0.86	346	1117856	80	13	45	22	145

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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	383
Total TN	78829644
Total FP	25573
Total FP CONTRA	3699
Total FP INCONS	21442
Total FP COMP	432
Total FN	29092

Total Scores
MCC	0.014
Average MCC ± 95% Confidence Intervals	0.014 ± 0.004
Sensitivity	0.013
Positive Predictive Value	0.015
Nr of predictions	62

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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_00306	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1445474	405	54	322	29	462
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1627675	437	70	357	10	494
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_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_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_00759	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	9	1636732	429	64	340	25	472
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
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 RNAalifold(seed) - scored higher in this pairwise comparison

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

2. Individual counts for RNAalifold(seed) [ 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 ]