CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RSpredict(20)		RSpredict(seed)
MCC	0.013	>	0.012
Average MCC ± 95% Confidence Intervals	0.014 ± 0.004	>	0.012 ± 0.004
Sensitivity	0.013	>	0.011
Positive Predictive Value	0.015	>	0.014
Total TP	319	>	272
Total TN	65503578	<	65505609
Total FP	21579	>	19547
Total FP CONTRA	3082	>	2913
Total FP INCONS	18144	>	16329
Total FP COMP	353	>	305
Total FN	24428	<	24475
P-value	5.62644058675e-08

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Performance plots

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

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Performance of RSpredict(20) - scored higher in this pairwise comparison

1. Total counts & total scores for RSpredict(20)

Total Base Pair Counts
Total TP	319
Total TN	65503578
Total FP	21579
Total FP CONTRA	3082
Total FP INCONS	18144
Total FP COMP	353
Total FN	24428

Total Scores
MCC	0.013
Average MCC ± 95% Confidence Intervals	0.014 ± 0.004
Sensitivity	0.013
Positive Predictive Value	0.015
Nr of predictions	52

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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_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_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_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_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_00379	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	2126541	465	66	346	53	534
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_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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Performance of RSpredict(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	272
Total TN	65505609
Total FP	19547
Total FP CONTRA	2913
Total FP INCONS	16329
Total FP COMP	305
Total FN	24475

Total Scores
MCC	0.012
Average MCC ± 95% Confidence Intervals	0.012 ± 0.004
Sensitivity	0.011
Positive Predictive Value	0.014
Nr of predictions	52

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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_00289	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1189252	396	60	332	4	467
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_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
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 RSpredict(20) - scored higher in this pairwise comparison

1. Total counts & total scores for RSpredict(20)

2. Individual counts for RSpredict(20) [ 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 ]