CompaRNA - on-line benchmarks of RNA structure prediction methods

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Overview

Metric	CentroidAlifold(20)		RSpredict(20)
MCC	0.726	>	0.012
Average MCC ± 95% Confidence Intervals	0.718 ± 0.036	>	0.013 ± 0.003
Sensitivity	0.614	>	0.012
Positive Predictive Value	0.860	>	0.014
Total TP	22679	>	436
Total TN	104344087	>	104338716
Total FP	5560	<	32060
Total FP CONTRA	629	<	4727
Total FP INCONS	3071	<	26587
Total FP COMP	1860	>	746
Total FN	14285	<	36528
P-value	3.56938820447e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	22679
Total TN	104344087
Total FP	5560
Total FP CONTRA	629
Total FP INCONS	3071
Total FP COMP	1860
Total FN	14285

Total Scores
MCC	0.726
Average MCC ± 95% Confidence Intervals	0.718 ± 0.036
Sensitivity	0.614
Positive Predictive Value	0.860
Nr of predictions	77

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2. Individual counts for CentroidAlifold(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...	0.91	0.86	0.95	394	1085188	51	6	13	32	64
CRW_00034	SSU_rRNA_bacteria links to Rfam database...	0.83	0.77	0.90	365	1141911	54	9	31	14	109
CRW_00048	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.93	374	1170812	45	10	19	16	96
CRW_00054	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.93	364	1107423	43	10	19	14	92
CRW_00059	SSU_rRNA_bacteria links to Rfam database...	0.85	0.78	0.93	368	1172351	42	9	18	15	105
CRW_00061	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.92	380	1181542	47	10	21	16	96
CRW_00068	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.91	365	1108906	48	11	23	14	92
CRW_00096	SSU_rRNA_bacteria links to Rfam database...	0.86	0.78	0.95	363	1178497	43	4	16	23	102
CRW_00140	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.92	372	1135875	46	11	20	15	91
CRW_00141	SSU_rRNA_bacteria links to Rfam database...	0.85	0.78	0.93	371	1201625	47	10	19	18	105
CRW_00150	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.92	372	1152515	48	10	24	14	94
CRW_00152	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.91	364	1180015	52	13	24	15	107
CRW_00166	SSU_rRNA_bacteria links to Rfam database...	0.86	0.78	0.94	364	1190809	45	4	19	22	104
CRW_00173	SSU_rRNA_bacteria links to Rfam database...	0.80	0.75	0.86	332	1082272	67	11	41	15	113
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.83	0.75	0.92	356	1178493	48	7	24	17	117
CRW_00196	SSU_rRNA_bacteria links to Rfam database...	0.86	0.79	0.94	377	1207832	45	8	18	19	98
CRW_00230	SSU_rRNA_bacteria links to Rfam database...	0.86	0.79	0.94	378	1198524	39	8	16	15	100
CRW_00245	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.93	367	1105932	46	9	20	17	86
CRW_00248	SSU_rRNA_bacteria links to Rfam database...	0.85	0.77	0.92	375	1218735	46	11	20	15	109
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.92	370	1198524	46	11	21	14	108
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.91	360	1192345	51	10	25	16	108
CRW_00270	SSU_rRNA_bacteria links to Rfam database...	0.86	0.80	0.92	362	1111893	46	11	20	15	93
CRW_00271	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.91	355	1122363	48	8	25	15	107
CRW_00273	SSU_rRNA_bacteria links to Rfam database...	0.86	0.79	0.92	354	1085218	46	8	21	17	92
CRW_00275	SSU_rRNA_bacteria links to Rfam database...	0.87	0.81	0.93	371	1114870	46	9	21	16	86
CRW_00277	SSU_rRNA_bacteria links to Rfam database...	0.85	0.78	0.91	354	1110408	50	12	21	17	99
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.84	0.78	0.91	351	1129869	54	7	29	18	99
CRW_00279	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.92	357	1180030	50	8	21	21	107
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.84	0.79	0.89	357	1117860	63	9	34	20	96
CRW_00281	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.92	357	1144951	49	9	24	16	107
CRW_00284	SSU_rRNA_bacteria links to Rfam database...	0.84	0.77	0.91	350	1131377	50	7	26	17	106
CRW_00285	SSU_rRNA_bacteria links to Rfam database...	0.83	0.77	0.90	353	1117869	56	11	27	18	105
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.82	0.75	0.91	356	1189260	53	9	28	16	120
CRW_00298	SSU_rRNA_eukarya links to Rfam database...	0.52	0.37	0.72	183	1620647	90	6	64	20	311
CRW_00301	SSU_rRNA_eukarya links to Rfam database...	0.47	0.34	0.64	178	1762223	133	11	91	31	341
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.52	0.37	0.73	171	1445616	97	6	57	34	291
CRW_00310	SSU_rRNA_eukarya links to Rfam database...	0.49	0.37	0.66	192	1805657	126	13	88	25	329
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.57	0.40	0.80	201	1627859	78	6	44	28	301
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.51	0.37	0.71	190	1988747	113	10	68	35	327
CRW_00332	SSU_rRNA_eukarya links to Rfam database...	0.48	0.34	0.67	161	1769781	123	8	71	44	316
CRW_00333	SSU_rRNA_eukarya links to Rfam database...	0.43	0.30	0.61	155	1892229	131	20	81	30	359
CRW_00345	SSU_rRNA_eukarya links to Rfam database...	0.51	0.36	0.72	181	1586621	96	8	61	27	317
CRW_00346	SSU_rRNA_eukarya links to Rfam database...	0.53	0.38	0.74	192	1584829	102	6	63	33	309
CRW_00348	SSU_rRNA_eukarya links to Rfam database...	0.54	0.40	0.72	200	1615226	107	10	67	30	303
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.53	0.39	0.73	196	1675098	99	8	63	28	311
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.52	0.37	0.71	180	1579501	100	8	64	28	302
CRW_00370	SSU_rRNA_eukarya links to Rfam database...	0.58	0.41	0.83	208	1640515	64	4	39	21	298
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.55	0.40	0.75	199	1611646	93	8	57	28	297
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.50	0.37	0.69	182	1626042	112	11	71	30	316
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.49	0.33	0.72	176	2126710	109	5	62	42	358
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.51	0.35	0.73	182	1751006	96	7	61	28	333
CRW_00403	SSU_rRNA_eukarya links to Rfam database...	0.52	0.39	0.70	180	1606270	126	11	67	48	284
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.51	0.38	0.68	189	1615224	117	8	82	27	307
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.48	0.34	0.67	170	1665972	109	11	72	26	325
CRW_00466	SSU_rRNA_bacteria links to Rfam database...	0.86	0.79	0.93	364	1116372	45	9	20	16	94
CRW_00589	SSU_rRNA_bacteria links to Rfam database...	0.86	0.78	0.94	347	1094091	45	2	20	23	98
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.86	0.79	0.93	359	1119369	53	3	25	25	93
CRW_00591	SSU_rRNA_bacteria links to Rfam database...	0.86	0.79	0.92	354	1098520	55	6	23	26	92
CRW_00598	SSU_rRNA_eukarya links to Rfam database...	0.49	0.34	0.70	169	1665982	103	5	69	29	322
CRW_00758	SSU_rRNA_eukarya links to Rfam database...	0.52	0.38	0.72	184	1640510	108	6	66	36	299
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.51	0.38	0.69	181	1636884	113	8	72	33	300
CRW_00760	SSU_rRNA_eukarya links to Rfam database...	0.52	0.37	0.74	180	1638713	102	7	55	40	306
CRW_00772	SSU_rRNA_bacteria links to Rfam database...	0.79	0.73	0.85	295	945652	81	5	48	28	109
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.83	0.76	0.91	340	1137411	63	5	30	28	107
CRW_00795	SSU_rRNA_bacteria links to Rfam database...	0.80	0.72	0.88	284	1152598	97	3	36	58	110
CRW_00849	SSU_rRNA_bacteria links to Rfam database...	0.82	0.76	0.88	357	1117854	65	10	39	16	113
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.85	0.80	0.91	369	1135873	50	13	23	14	95
CRW_01153	SSU_rRNA_eukarya links to Rfam database...	0.50	0.36	0.69	179	1606270	108	8	71	29	324
CRW_01171	SSU_rRNA_eukarya links to Rfam database...	0.49	0.36	0.67	183	1593733	116	11	78	27	323
CRW_01300	SSU_rRNA_eukarya links to Rfam database...	0.55	0.40	0.76	205	1693451	88	6	58	24	310
PDB_00703	SSU_rRNA_bacteria links to Rfam database...	0.81	0.70	0.92	348	1073468	55	8	21	26	147
PDB_00854	SSU_rRNA_bacteria links to Rfam database...	0.77	0.65	0.90	348	1500393	73	4	33	36	187
PDB_01088	SSU_rRNA_bacteria links to Rfam database...	0.75	0.62	0.90	341	1471090	76	2	37	37	206
PDB_01103	SSU_rRNA_bacteria links to Rfam database...	0.77	0.64	0.92	361	1606134	59	8	25	26	201
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.78	0.66	0.92	359	1433581	59	2	29	28	181
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.79	0.68	0.92	357	1204739	53	7	25	21	170
PDB_01273	SSU_rRNA_bacteria links to Rfam database...	0.80	0.69	0.91	341	1117886	62	6	27	29	150

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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	436
Total TN	104338716
Total FP	32060
Total FP CONTRA	4727
Total FP INCONS	26587
Total FP COMP	746
Total FN	36528

Total Scores
MCC	0.012
Average MCC ± 95% Confidence Intervals	0.013 ± 0.003
Sensitivity	0.012
Positive Predictive Value	0.014
Nr of predictions	77

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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_00298	SSU_rRNA_eukarya links to Rfam database...	0.01	0.01	0.01	3	1620508	410	63	326	21	491
CRW_00301	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1762034	472	82	379	11	511
CRW_00306	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1445474	405	54	322	29	462
CRW_00310	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1805520	442	63	359	20	513
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1627675	437	70	357	10	494
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1988575	477	82	350	45	509
CRW_00332	SSU_rRNA_eukarya links to Rfam database...	0.01	0.01	0.01	3	1769654	389	59	305	25	474
CRW_00333	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	1	1892051	454	80	353	21	513
CRW_00345	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1586488	384	57	318	9	490
CRW_00346	SSU_rRNA_eukarya links to Rfam database...	0.01	0.01	0.01	4	1584683	432	63	340	29	497
CRW_00348	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1615104	410	69	330	11	503
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1674979	406	62	324	20	507
CRW_00366	SSU_rRNA_eukarya links to Rfam database...	0.01	0.01	0.01	4	1579393	371	66	290	15	478
CRW_00370	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	10	1640309	469	52	395	22	496
CRW_00371	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1611495	424	63	344	17	488
CRW_00372	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1625926	390	51	321	18	490
CRW_00379	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	2126541	465	66	346	53	534
CRW_00386	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1750835	427	65	348	14	507
CRW_00403	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1606168	385	68	292	25	464
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_00598	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1665800	449	72	353	24	491
CRW_00758	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1640340	444	79	347	18	483
CRW_00759	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	9	1636732	429	64	340	25	472
CRW_00760	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1638553	425	77	325	23	486
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
CRW_01300	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1693285	445	62	373	10	515
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 CentroidAlifold(20) - scored higher in this pairwise comparison

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

2. Individual counts for CentroidAlifold(20) [ 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 ]