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(seed)		RSpredict(20)
MCC	0.665	>	0.014
Average MCC ± 95% Confidence Intervals	0.668 ± 0.027	>	0.014 ± 0.004
Sensitivity	0.595	>	0.013
Positive Predictive Value	0.743	>	0.015
Total TP	16336	>	359
Total TN	72152147	>	72150229
Total FP	8016	<	23913
Total FP CONTRA	849	<	3451
Total FP INCONS	4799	<	20092
Total FP COMP	2368	>	370
Total FN	11117	<	27094
P-value	3.56938820447e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	16336
Total TN	72152147
Total FP	8016
Total FP CONTRA	849
Total FP INCONS	4799
Total FP COMP	2368
Total FN	11117

Total Scores
MCC	0.665
Average MCC ± 95% Confidence Intervals	0.668 ± 0.027
Sensitivity	0.595
Positive Predictive Value	0.743
Nr of predictions	58

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2. Individual counts for MXScarna(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...	0.83	0.81	0.86	369	1085172	112	11	49	52	89
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.68	0.60	0.78	285	1141950	117	9	72	36	189
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.74	0.68	0.82	318	1170827	101	10	60	31	152
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.73	0.66	0.81	302	1107443	101	13	58	30	154
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.72	0.64	0.81	305	1172369	105	12	60	33	168
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.73	0.66	0.81	312	1181569	104	11	61	32	164
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.74	0.67	0.82	305	1108933	99	12	55	32	152
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.72	0.65	0.81	301	1178507	110	5	67	38	164
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.73	0.66	0.81	304	1135902	106	11	61	34	159
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.73	0.66	0.82	312	1201645	103	12	56	35	164
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.72	0.64	0.81	300	1152549	106	11	61	34	166
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.74	0.68	0.82	319	1180025	107	12	60	35	152
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.73	0.65	0.82	305	1190824	106	6	61	39	163
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.65	0.59	0.72	264	1082289	130	14	89	27	181
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.68	0.61	0.77	287	1178505	117	12	76	29	186
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.76	0.69	0.83	327	1207841	102	11	56	35	148
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.75	0.67	0.83	321	1198539	99	12	54	33	157
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.73	0.66	0.81	299	1105958	104	12	59	33	154
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.72	0.64	0.81	311	1218757	105	11	62	32	173
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.71	0.64	0.78	307	1198533	120	11	75	34	171
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.74	0.66	0.82	311	1192362	98	11	56	31	157
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.74	0.67	0.82	304	1111915	100	11	56	33	151
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.71	0.64	0.80	295	1122381	105	12	63	30	167
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.72	0.65	0.80	290	1085237	110	10	64	36	156
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.74	0.67	0.82	306	1114897	103	10	58	35	151
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.73	0.66	0.80	300	1110421	108	12	62	34	153
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.68	0.60	0.78	271	1129907	113	9	69	35	179
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.72	0.64	0.81	299	1180047	107	10	60	37	165
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.70	0.63	0.79	284	1117899	114	10	67	37	169
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.73	0.66	0.82	305	1144968	102	10	58	34	159
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.73	0.65	0.81	297	1131394	104	10	59	35	159
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.71	0.64	0.79	294	1117886	113	13	67	33	164
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.68	0.60	0.77	287	1189280	118	12	74	32	189
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.42	0.39	0.46	181	1445456	267	46	167	54	281
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.48	0.45	0.51	215	1579331	275	41	166	68	267
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.50	0.47	0.53	232	1611469	276	42	167	67	264
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.36	0.32	0.41	170	2126540	318	50	193	75	364
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.49	0.47	0.52	231	1615062	273	41	169	63	265
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.46	0.43	0.49	213	1665792	286	43	177	66	282
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.74	0.66	0.82	304	1116392	101	11	58	32	154
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.70	0.63	0.79	279	1094105	117	6	70	41	166
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.73	0.65	0.82	294	1119399	104	6	57	41	158
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.74	0.66	0.82	294	1098545	110	6	58	46	152
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.45	0.42	0.48	201	1636722	295	39	183	73	280
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.63	0.55	0.72	223	945690	133	6	81	46	181
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.71	0.63	0.80	280	1137437	111	7	62	42	167
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.63	0.55	0.72	216	1152623	164	8	74	82	178
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.67	0.59	0.76	279	1117895	114	13	73	28	191
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.72	0.65	0.80	301	1135902	107	11	64	32	163
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.47	0.44	0.50	221	1606085	276	37	185	54	282
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.49	0.46	0.53	231	1593565	264	35	174	55	275
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.66	0.56	0.77	278	1073486	114	9	72	33	217
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.63	0.52	0.77	280	1500414	135	2	82	51	255
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.61	0.49	0.76	269	1471116	131	6	79	46	278
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.57	0.47	0.69	263	1606145	154	8	112	34	299
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.66	0.55	0.80	299	1433595	117	1	76	40	241
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.66	0.56	0.79	296	1204752	112	8	72	32	231
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.69	0.59	0.80	290	1117898	113	9	63	41	201

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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	359
Total TN	72150229
Total FP	23913
Total FP CONTRA	3451
Total FP INCONS	20092
Total FP COMP	370
Total FN	27094

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	58

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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_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_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 MXScarna(seed) - scored higher in this pairwise comparison

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

2. Individual counts for MXScarna(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 ]