CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	PETfold_pre2.0(seed)		RSpredict(seed)
MCC	0.801	>	0.012
Average MCC ± 95% Confidence Intervals	0.803 ± 0.020	>	0.012 ± 0.003
Sensitivity	0.773	>	0.011
Positive Predictive Value	0.831	>	0.014
Total TP	20805	>	302
Total TN	71036304	<	71039984
Total FP	6889	<	21410
Total FP CONTRA	769	<	3177
Total FP INCONS	3466	<	17881
Total FP COMP	2654	>	352
Total FN	6099	<	26602
P-value	3.56938820447e-08

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Performance plots

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

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Performance of PETfold_pre2.0(seed) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	20805
Total TN	71036304
Total FP	6889
Total FP CONTRA	769
Total FP INCONS	3466
Total FP COMP	2654
Total FN	6099

Total Scores
MCC	0.801
Average MCC ± 95% Confidence Intervals	0.803 ± 0.020
Sensitivity	0.773
Positive Predictive Value	0.831
Nr of predictions	57

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2. Individual counts for PETfold_pre2.0(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...	0.89	0.88	0.90	405	1085153	80	10	33	37	53
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.85	0.84	0.87	395	1170759	96	18	43	35	75
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.86	0.86	0.87	390	1107367	95	16	43	36	66
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.85	0.83	0.87	392	1172293	95	17	44	34	81
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.84	0.82	0.86	388	1181504	96	16	45	35	88
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.86	0.86	0.87	394	1108851	94	17	43	34	63
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.86	0.84	0.88	392	1178434	98	11	43	44	73
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.85	0.84	0.86	387	1135829	97	15	47	35	76
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.85	0.82	0.87	392	1201573	98	16	44	38	84
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.85	0.83	0.87	385	1152477	92	16	43	33	81
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.84	0.82	0.86	386	1179969	96	16	45	35	85
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.86	0.84	0.88	393	1190749	97	11	43	43	75
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.80	0.79	0.81	353	1082222	118	17	64	37	92
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.84	0.82	0.86	386	1178430	105	17	47	41	87
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.83	0.81	0.86	384	1207786	102	15	50	37	91
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.84	0.82	0.87	392	1198473	97	16	45	36	86
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.86	0.86	0.87	388	1105880	95	18	42	35	65
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.83	0.80	0.86	388	1218691	98	16	46	36	96
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.84	0.82	0.87	391	1198474	97	16	45	36	87
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.85	0.82	0.87	386	1192295	93	16	43	34	82
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.87	0.86	0.87	391	1111838	94	15	42	37	64
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.83	0.82	0.85	378	1122307	105	14	52	39	84
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.86	0.85	0.86	380	1085161	98	14	46	38	66
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.86	0.85	0.87	390	1114823	98	15	43	40	67
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.84	0.83	0.85	377	1110354	101	16	48	37	76
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.84	0.83	0.85	377	1117815	109	16	52	41	76
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.85	0.84	0.87	388	1144894	97	16	43	38	76
CRW_00283	SSU_rRNA_bacteria links to Rfam database...	0.78	0.77	0.80	331	1015610	118	18	66	34	101
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.82	0.80	0.84	382	1189200	109	16	55	38	94
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.74	0.72	0.77	332	1123817	133	22	79	32	129
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.68	0.66	0.70	305	1445417	186	15	113	58	157
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.65	0.62	0.68	300	1579311	211	15	127	69	182
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.68	0.65	0.71	322	1611455	199	13	120	66	174
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.60	0.54	0.66	286	2126521	223	18	128	77	248
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.67	0.64	0.71	318	1615053	200	15	117	68	178
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.64	0.61	0.67	303	1665770	223	20	132	71	192
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.86	0.85	0.87	391	1116315	99	14	45	40	67
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.87	0.84	0.89	376	1094037	99	6	41	52	69
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.87	0.84	0.89	381	1119327	104	6	42	56	71
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.87	0.86	0.89	382	1098473	103	6	42	55	64
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.65	0.62	0.68	297	1636709	218	15	124	79	184
CRW_00763	SSU_rRNA_bacteria links to Rfam database...	0.83	0.80	0.87	357	1215610	110	5	48	57	89
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.84	0.83	0.85	317	1201654	139	6	48	85	67
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.83	0.81	0.86	362	1137365	112	11	48	53	85
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.79	0.76	0.82	299	1152557	159	6	59	94	95
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.79	0.76	0.81	359	1117819	116	16	66	34	111
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.86	0.85	0.87	395	1135823	93	17	43	33	69
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.61	0.58	0.64	294	1606070	223	18	146	59	209
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.63	0.60	0.67	304	1593548	214	15	138	61	202
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.87	0.85	0.89	367	977489	81	8	37	36	67
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.79	0.73	0.86	361	1073423	107	9	52	46	134
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.76	0.68	0.86	364	1500354	120	9	51	60	171
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.75	0.67	0.85	365	1471040	119	5	60	54	182
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.76	0.67	0.86	376	1606090	108	8	54	46	186
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.77	0.70	0.86	376	1433534	108	3	58	47	164
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.80	0.73	0.86	387	1204680	102	10	51	41	140
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.80	0.75	0.86	368	1117832	112	8	52	52	123

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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 PETfold_pre2.0(seed) - scored higher in this pairwise comparison

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

2. Individual counts for PETfold_pre2.0(seed) [ 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 ]