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(seed)
MCC	0.818	>	0.012
Average MCC ± 95% Confidence Intervals	0.819 ± 0.044	>	0.012 ± 0.003
Sensitivity	0.775	>	0.011
Positive Predictive Value	0.864	>	0.014
Total TP	20859	>	302
Total TN	71037192	<	71039984
Total FP	4172	<	21410
Total FP CONTRA	575	<	3177
Total FP INCONS	2718	<	17881
Total FP COMP	879	>	352
Total FN	6045	<	26602
P-value	3.56938820447e-08

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Performance plots

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

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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	20859
Total TN	71037192
Total FP	4172
Total FP CONTRA	575
Total FP INCONS	2718
Total FP COMP	879
Total FN	6045

Total Scores
MCC	0.818
Average MCC ± 95% Confidence Intervals	0.819 ± 0.044
Sensitivity	0.775
Positive Predictive Value	0.864
Nr of predictions	57

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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_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_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_00283	SSU_rRNA_bacteria links to Rfam database...	0.75	0.69	0.81	298	1015659	88	12	56	20	134
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.90	382	1189229	44	4	38	2	94
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.76	0.70	0.81	325	1123851	81	12	62	7	136
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.37	0.36	0.37	168	1445399	304	63	220	21	294
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.45	0.42	0.48	202	1579334	251	36	181	34	280
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.56	0.53	0.58	263	1611460	230	33	154	43	233
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.62	0.59	0.65	314	2126472	237	36	131	70	220
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_00759	SSU_rRNA_eukarya links to Rfam database...	0.40	0.38	0.42	181	1636714	284	45	205	34	300
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.75	0.69	0.82	306	1215649	111	12	53	46	140
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.71	0.64	0.79	246	1201714	124	13	52	59	138
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_01343	SSU_rRNA_archaea links to Rfam database...	0.82	0.76	0.89	328	977531	59	6	36	17	106
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(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	302
Total TN	71039984
Total FP	21410
Total FP CONTRA	3177
Total FP INCONS	17881
Total FP COMP	352
Total FN	26602

Total Scores
MCC	0.012
Average MCC ± 95% Confidence Intervals	0.012 ± 0.003
Sensitivity	0.011
Positive Predictive Value	0.014
Nr of predictions	57

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2. Individual counts for RSpredict(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...	0.00	0.00	0.00	0	1085147	454	58	396	0	458
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1170823	393	56	336	1	470
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1107442	369	56	309	4	447
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1172351	389	70	316	3	464
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1181549	397	64	331	2	467
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1108929	368	61	306	1	448
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1178474	406	51	355	0	465
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1135894	379	57	318	4	454
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	10	1201613	405	59	343	3	466
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1152527	398	50	344	4	466
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.01	0.01	0.01	3	1180016	399	56	341	2	468
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1190789	408	55	352	1	468
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	1	1082302	361	46	307	8	444
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1178475	411	54	351	6	473
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	8	1207825	403	55	347	1	467
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1198522	397	65	330	2	469
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1105951	369	62	306	1	444
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1218721	423	52	368	3	484
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1198517	412	51	358	3	478
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1192358	394	66	316	12	468
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1111909	369	63	305	1	446
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.04	0.03	0.04	16	1122383	354	58	294	2	446
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.03	0.02	0.03	11	1085239	353	59	292	2	435
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1114898	365	61	303	1	448
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.04	0.04	0.04	16	1110429	352	54	296	2	437
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1117885	368	54	312	2	444
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1144967	366	62	303	1	455
CRW_00283	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1015663	366	41	321	4	432
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1189252	396	60	332	4	467
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.03	0.02	0.03	11	1123875	370	46	318	6	450
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1445558	306	53	239	14	462
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1579464	301	50	239	12	482
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1611598	319	50	262	7	496
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	2126581	414	77	295	42	534
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1615206	309	45	252	12	496
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1665933	312	53	239	20	495
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1116386	371	63	307	1	449
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.04	0.04	0.04	16	1094092	354	55	297	2	429
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1119377	371	50	320	1	443
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1098530	368	58	306	4	437
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	1	1636859	310	50	235	25	480
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	1	1215655	374	61	303	10	445
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1201664	378	83	269	26	375
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1137386	398	62	329	7	438
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.04	0.04	0.04	15	1152569	351	71	266	14	379
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1117886	369	53	312	4	461
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1135900	370	64	305	1	455
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1606225	319	65	238	16	503
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1593701	318	50	254	14	506
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.02	0.02	0.02	9	977518	375	33	341	1	425
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1073471	365	45	320	0	486
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1500362	424	57	359	8	535
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1471050	425	45	375	5	547
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	1	1606120	411	54	353	4	561
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1433563	415	44	364	7	540
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.01	0.01	0.01	3	1204725	405	40	360	5	524
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1117880	384	44	336	4	491

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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(seed) - scored lower in this pairwise comparison

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

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