CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAfold		McQFold
MCC	0.492	>	0.417
Average MCC ± 95% Confidence Intervals	0.560 ± 0.081	<	0.614 ± 0.098
Sensitivity	0.531	>	0.398
Positive Predictive Value	0.456	>	0.438
Total TP	2030	>	1523
Total TN	5849682	<	5850656
Total FP	2962	>	2187
Total FP CONTRA	704	>	441
Total FP INCONS	1719	>	1515
Total FP COMP	539	>	231
Total FN	1795	<	2302
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RNAfold and McQFold. 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 RNAfold and McQFold).
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 RNAfold and McQFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAfold and McQFold. 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 RNAfold and McQFold).

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Performance of RNAfold - scored higher in this pairwise comparison

1. Total counts & total scores for RNAfold

Total Base Pair Counts
Total TP	2030
Total TN	5849682
Total FP	2962
Total FP CONTRA	704
Total FP INCONS	1719
Total FP COMP	539
Total FN	1795

Total Scores
MCC	0.492
Average MCC ± 95% Confidence Intervals	0.560 ± 0.081
Sensitivity	0.531
Positive Predictive Value	0.456
Nr of predictions	46

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2. Individual counts for RNAfold [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	-0.03	0.00	0.00	0	229	7	1	6	0	8
2KRL_A	-	0.91	0.87	0.95	20	2003	9	1	0	8	3
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	0	5	0	7
2M58_A	-	0.40	0.42	0.42	5	532	7	1	6	0	7
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2WDL_A	-	0.49	0.52	0.47	408	1444460	493	86	368	39	380
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	3	2	0	1	1
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.35	0.36	0.36	12	1786	22	1	20	1	21
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.81	0.79	0.85	22	1423	5	2	2	1	6
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.69	0.68	0.70	19	1445	9	1	7	1	9
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.17	17	22340	95	45	38	12	34
3IZ4_A	tmRNA links to Rfam database...	0.56	0.60	0.52	57	25426	57	26	27	4	38
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.56	0.58	0.54	238	421930	251	36	164	51	174
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J3D_C	tRNA links to Rfam database...	0.33	0.37	0.32	7	946	15	3	12	0	12
3J3E_8	5_8S_rRNA links to Rfam database...	0.25	0.33	0.20	5	2717	31	7	13	11	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.42	0.27	8	4731	42	10	12	20	11
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1089	22	4	18	0	20
3JYX_5	-	0.36	0.46	0.29	220	1968243	783	251	288	244	261
3KIY_A	-	0.50	0.53	0.48	414	1485013	501	90	363	48	372
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.91	0.86	0.97	32	2245	5	1	0	4	5
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	35	6	15	14	11
3PDR_A	ykoK links to Rfam database...	0.90	0.90	0.90	45	4790	7	2	3	2	5
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.77	0.76	0.79	22	1505	6	4	2	0	7
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.60	0.61	0.61	20	1956	14	4	9	1	13
3ZEX_B	-	0.35	0.39	0.32	136	420925	333	77	214	42	210
3ZEX_C	5_8S_rRNA links to Rfam database...	0.30	0.34	0.26	10	5336	43	5	23	15	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4482	43	11	18	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.59	0.57	0.62	16	1822	10	2	8	0	12
4JF2_A	preQ1-II links to Rfam database...	0.86	0.79	0.95	19	1062	1	1	0	0	5
4JRC_A	-	0.34	0.35	0.35	6	605	11	0	11	0	11

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Performance of McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

Total Base Pair Counts
Total TP	1523
Total TN	5850656
Total FP	2187
Total FP CONTRA	441
Total FP INCONS	1515
Total FP COMP	231
Total FN	2302

Total Scores
MCC	0.417
Average MCC ± 95% Confidence Intervals	0.614 ± 0.098
Sensitivity	0.398
Positive Predictive Value	0.438
Nr of predictions	46

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2. Individual counts for McQFold [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	0.79	0.63	1.00	5	231	0	0	0	0	3
2KRL_A	-	0.75	0.83	0.68	19	1996	15	7	2	6	4
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	1	4	0	7
2M58_A	-	0.60	0.58	0.64	7	533	5	1	3	1	5
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2WDL_A	-	0.37	0.37	0.36	294	1444515	545	84	429	32	494
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	2	2	0	0	1
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.98	0.97	1.00	32	1787	1	0	0	1	1
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.56	0.57	0.57	16	1421	13	4	8	1	12
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.21	0.21	0.24	6	1447	19	2	17	0	22
3IYQ_A	tmRNA links to Rfam database...	0.22	0.31	0.15	16	22335	100	45	44	11	35
3IZ4_A	tmRNA links to Rfam database...	0.46	0.46	0.47	44	25442	56	14	36	6	51
3J0L_a	-	0.21	0.18	0.29	2	404	6	3	2	1	9
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.55	0.56	0.55	231	421948	234	41	148	45	181
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2718	36	8	16	12	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.31	0.42	0.23	8	4726	41	12	15	14	11
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1091	20	4	16	0	20
3JYX_5	-	0.00	0.00	0.00	0	1969002	0	0	0	0	481
3KIY_A	-	0.38	0.38	0.38	302	1485090	544	83	405	56	484
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.42	0.42	0.44	8	717	10	2	8	0	11
3NPB_A	SAM links to Rfam database...	0.90	0.81	1.00	30	2248	5	0	0	5	7
3O58_3	5_8S_rRNA links to Rfam database...	0.30	0.36	0.25	8	4732	27	15	9	3	14
3PDR_A	ykoK links to Rfam database...	0.83	0.80	0.87	40	4794	9	2	4	3	10
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.82	0.83	0.83	24	1504	5	1	4	0	5
3U4M_B	-	0.95	0.91	1.00	20	1256	2	0	0	2	2
3W1K_J	tRNA-Sec links to Rfam database...	0.86	0.77	0.96	24	1653	1	1	0	0	7
3W3S_B	tRNA-Sec links to Rfam database...	0.49	0.45	0.54	15	1961	14	1	12	1	18
3ZEX_B	-	0.12	0.14	0.12	47	420944	379	78	283	18	299
3ZEX_C	5_8S_rRNA links to Rfam database...	0.33	0.34	0.32	10	5343	25	4	17	4	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	33	11	16	6	15
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ATO_G	-	-0.03	0.00	0.00	0	215	5	0	5	0	7
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FRG_B	AdoCbl-variant links to Rfam database...	0.93	0.88	1.00	21	1181	0	0	0	0	3
4FRN_A	AdoCbl-variant links to Rfam database...	0.82	0.71	0.95	20	1827	1	1	0	0	8
4JF2_A	preQ1-II links to Rfam database...	0.92	1.00	0.86	24	1054	5	4	0	1	0
4JRC_A	-	0.97	0.94	1.00	16	606	0	0	0	0	1

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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 RNAfold - scored higher in this pairwise comparison

1. Total counts & total scores for RNAfold

2. Individual counts for RNAfold [ download as .csv ]

Performance of McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

2. Individual counts for McQFold [ download as .csv ]