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(seed)
MCC	0.661	>	0.012
Average MCC ± 95% Confidence Intervals	0.665 ± 0.027	>	0.012 ± 0.003
Sensitivity	0.592	>	0.011
Positive Predictive Value	0.739	>	0.014
Total TP	15922	>	302
Total TN	71039805	<	71039984
Total FP	7979	<	21410
Total FP CONTRA	837	<	3177
Total FP INCONS	4780	<	17881
Total FP COMP	2362	>	352
Total FN	10982	<	26602
P-value	3.56938820447e-08

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Performance plots

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

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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	15922
Total TN	71039805
Total FP	7979
Total FP CONTRA	837
Total FP INCONS	4780
Total FP COMP	2362
Total FN	10982

Total Scores
MCC	0.661
Average MCC ± 95% Confidence Intervals	0.665 ± 0.027
Sensitivity	0.592
Positive Predictive Value	0.739
Nr of predictions	57

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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_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_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_00283	SSU_rRNA_bacteria links to Rfam database...	0.63	0.56	0.71	242	1015684	127	13	86	28	190
CRW_00289	SSU_rRNA_bacteria links to Rfam database...	0.68	0.60	0.77	287	1189280	118	12	74	32	189
CRW_00292	SSU_rRNA_bacteria links to Rfam database...	0.62	0.53	0.71	245	1123906	126	12	87	27	216
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_00763	SSU_rRNA_bacteria links to Rfam database...	0.68	0.59	0.78	262	1215683	119	6	69	44	184
CRW_00778	SSU_rRNA_bacteria links to Rfam database...	0.63	0.55	0.73	212	1201733	150	4	76	70	172
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
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.73	0.68	0.78	294	977526	128	10	71	47	140
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(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 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(seed) - scored lower in this pairwise comparison

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

2. Individual counts for RSpredict(seed) [ download as .csv ]