CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MXScarna(20)		RSpredict(seed)
MCC	0.645	>	0.012
Average MCC ± 95% Confidence Intervals	0.648 ± 0.031	>	0.012 ± 0.004
Sensitivity	0.589	>	0.011
Positive Predictive Value	0.707	>	0.014
Total TP	14570	>	272
Total TN	65504501	<	65505609
Total FP	8269	<	19547
Total FP CONTRA	919	<	2913
Total FP INCONS	5133	<	16329
Total FP COMP	2217	>	305
Total FN	10177	<	24475
P-value	3.56938820447e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	14570
Total TN	65504501
Total FP	8269
Total FP CONTRA	919
Total FP INCONS	5133
Total FP COMP	2217
Total FN	10177

Total Scores
MCC	0.645
Average MCC ± 95% Confidence Intervals	0.648 ± 0.031
Sensitivity	0.589
Positive Predictive Value	0.707
Nr of predictions	52

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2. Individual counts for MXScarna(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...	0.84	0.81	0.87	369	1085176	107	10	46	51	89
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.72	0.67	0.78	317	1170807	127	11	80	36	153
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.68	0.63	0.74	288	1107425	137	16	87	34	168
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.72	0.66	0.78	312	1172344	127	16	74	37	161
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.73	0.66	0.81	316	1181563	109	13	61	35	160
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.69	0.64	0.74	293	1108909	137	18	85	34	164
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.75	0.68	0.81	318	1178489	108	6	67	35	147
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.76	0.71	0.81	328	1135874	114	12	64	38	135
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.69	0.64	0.75	305	1201619	132	14	87	31	171
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.72	0.65	0.80	303	1152540	113	14	64	35	163
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.76	0.70	0.82	332	1180009	110	11	64	35	139
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.65	0.60	0.71	281	1190800	160	10	105	45	187
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.57	0.52	0.63	232	1082285	168	19	120	29	213
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.62	0.56	0.68	264	1178492	152	16	108	28	209
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.73	0.67	0.80	319	1207837	117	10	69	38	156
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.73	0.67	0.80	319	1198526	122	12	69	41	159
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.73	0.67	0.81	302	1105955	106	13	58	35	151
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.71	0.65	0.77	317	1218729	129	13	82	34	167
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.73	0.67	0.79	321	1198521	119	12	72	35	157
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.70	0.64	0.77	299	1192353	124	11	77	36	169
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.72	0.67	0.77	306	1111891	121	14	75	32	149
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.70	0.65	0.77	298	1122364	122	17	72	33	164
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.68	0.62	0.74	277	1085225	135	13	86	36	169
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.71	0.63	0.80	289	1114908	114	13	61	40	168
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.68	0.63	0.73	286	1110405	132	17	87	28	167
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.72	0.66	0.78	301	1117875	125	10	74	41	152
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.71	0.65	0.78	303	1144954	117	13	71	33	161
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.62	0.58	0.66	274	1189239	172	18	122	32	202
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.43	0.40	0.46	183	1445453	276	47	167	62	279
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.42	0.40	0.43	195	1579299	332	47	212	73	287
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.49	0.46	0.53	229	1611474	266	39	168	59	267
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.37	0.33	0.42	175	2126532	323	40	206	77	359
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.49	0.46	0.52	227	1615066	271	42	168	61	269
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.39	0.37	0.41	181	1665782	316	50	212	54	314
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.63	0.58	0.69	266	1116382	147	16	101	30	192
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.69	0.62	0.76	277	1094097	130	6	80	44	168
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.72	0.67	0.78	303	1119366	134	11	76	47	149
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.74	0.68	0.81	303	1098531	115	7	62	46	143
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.42	0.40	0.44	191	1636712	314	43	199	72	290
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.67	0.60	0.75	268	1137427	134	8	83	43	179
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.63	0.57	0.71	224	1152605	176	10	82	84	170
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.61	0.55	0.68	260	1117878	154	17	105	32	210
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.74	0.69	0.79	322	1135872	121	12	72	37	142
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.44	0.42	0.46	211	1606072	295	46	199	50	292
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.48	0.45	0.51	229	1593556	274	47	173	54	277
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.69	0.60	0.79	295	1073472	114	10	68	36	200
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.62	0.51	0.75	274	1500415	142	2	87	53	261
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.66	0.56	0.78	308	1471077	135	7	78	50	239
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.61	0.52	0.71	293	1606118	156	16	101	39	269
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.64	0.54	0.75	291	1433583	134	3	94	37	249
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.66	0.57	0.76	302	1204732	134	11	83	40	225
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.69	0.60	0.79	294	1117886	120	10	70	40	197

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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 MXScarna(20) - scored higher in this pairwise comparison

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

2. Individual counts for MXScarna(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 ]