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)		McQFold
MCC	0.624	>	0.539
Average MCC ± 95% Confidence Intervals	0.637 ± 0.064	>	0.586 ± 0.098
Sensitivity	0.518	>	0.462
Positive Predictive Value	0.756	>	0.633
Total TP	676	>	603
Total TN	247566	>	247508
Total FP	304	<	397
Total FP CONTRA	38	<	54
Total FP INCONS	180	<	295
Total FP COMP	86	>	48
Total FN	629	<	702
P-value	5.23657817852e-08

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Performance plots

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

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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	676
Total TN	247566
Total FP	304
Total FP CONTRA	38
Total FP INCONS	180
Total FP COMP	86
Total FN	629

Total Scores
MCC	0.624
Average MCC ± 95% Confidence Intervals	0.637 ± 0.064
Sensitivity	0.518
Positive Predictive Value	0.756
Nr of predictions	34

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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
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.73	0.70	0.78	14	972	4	0	4	0	6
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	4	4556	3	0	0	3	16
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.80	0.71	0.91	30	5118	4	0	3	1	12
3A2K_C	tRNA links to Rfam database...	0.66	0.57	0.76	16	2905	6	1	4	1	12
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	2	0	0	2	7
3G4S_9	5S_rRNA links to Rfam database...	0.52	0.40	0.68	23	7347	13	1	10	2	34
3GX2_A	SAM links to Rfam database...	0.70	0.58	0.85	23	4344	5	0	4	1	17
3IVN_B	Purine links to Rfam database...	0.74	0.58	0.95	18	2327	1	1	0	0	13
3IZ4_A	tmRNA links to Rfam database...	0.51	0.41	0.64	54	70791	32	7	24	1	78
3IZF_C	5S_rRNA links to Rfam database...	0.67	0.59	0.76	32	6861	11	1	9	1	22
3J20_0	tRNA links to Rfam database...	0.82	0.67	1.00	20	2830	0	0	0	0	10
3J20_1	tRNA links to Rfam database...	0.93	0.87	1.00	20	2906	0	0	0	0	3
3J2L_3	5S_rRNA links to Rfam database...	0.54	0.42	0.71	22	7844	11	1	8	2	31
3JYV_7	tRNA links to Rfam database...	0.79	0.63	1.00	20	2830	0	0	0	0	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.33	0.30	0.37	10	12219	32	2	15	15	23
3JYX_3	5S_rRNA links to Rfam database...	0.55	0.52	0.58	14	6304	23	0	10	13	13
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.69	0.59	0.82	27	6988	9	1	5	3	19
3O58_2	5S_rRNA links to Rfam database...	0.74	0.74	0.74	28	7222	13	4	6	3	10
3O58_3	5_8S_rRNA links to Rfam database...	0.52	0.40	0.67	14	12382	17	2	5	10	21
3PDR_A	ykoK links to Rfam database...	0.71	0.57	0.89	41	12834	9	0	5	4	31
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.63	0.55	0.74	23	3885	8	2	6	0	19
3ZEX_C	5_8S_rRNA links to Rfam database...	0.31	0.21	0.46	11	14172	13	2	11	0	41
3ZEX_D	5S_rRNA links to Rfam database...	0.68	0.63	0.74	31	6979	11	2	9	0	18
4A1C_3	5S_rRNA links to Rfam database...	0.64	0.56	0.75	30	7100	11	2	8	1	24
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	36	2	17	17	28
4AOB_A	SAM links to Rfam database...	0.62	0.55	0.72	23	4339	10	0	9	1	19
4ENB_A	crcB links to Rfam database...	0.26	0.11	0.67	2	1272	1	0	1	0	17
4ENC_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1319	0	0	0	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	0.55	0.44	0.70	14	3466	6	2	4	0	18

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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	603
Total TN	247508
Total FP	397
Total FP CONTRA	54
Total FP INCONS	295
Total FP COMP	48
Total FN	702

Total Scores
MCC	0.539
Average MCC ± 95% Confidence Intervals	0.586 ± 0.098
Sensitivity	0.462
Positive Predictive Value	0.633
Nr of predictions	34

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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
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.31	0.30	0.33	6	4542	25	1	11	13	14
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.27	0.24	0.32	10	5120	21	0	21	0	32
3A2K_C	tRNA links to Rfam database...	0.86	0.75	1.00	21	2905	0	0	0	0	7
3AMU_B	tRNA links to Rfam database...	0.75	0.59	0.94	16	2986	3	0	1	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.27	0.21	0.36	12	7348	21	1	20	0	45
3GX2_A	SAM links to Rfam database...	0.47	0.40	0.57	16	4343	13	1	11	1	24
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IZ4_A	tmRNA links to Rfam database...	0.42	0.36	0.49	47	70780	53	6	43	4	85
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	6867	6	0	6	0	24
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.20	0.21	0.19	7	12210	33	8	21	4	26
3JYX_3	5S_rRNA links to Rfam database...	0.21	0.22	0.20	6	6298	24	9	15	0	21
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.81	0.67	0.97	31	6989	4	1	0	3	15
3O58_2	5S_rRNA links to Rfam database...	0.83	0.71	0.96	27	7232	2	0	1	1	11
3O58_3	5_8S_rRNA links to Rfam database...	0.26	0.26	0.26	9	12368	26	10	16	0	26
3PDR_A	ykoK links to Rfam database...	0.69	0.56	0.87	40	12834	9	0	6	3	32
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.71	0.60	0.86	25	3887	4	0	4	0	17
3ZEX_C	5_8S_rRNA links to Rfam database...	0.27	0.21	0.34	11	14164	24	2	19	3	41
3ZEX_D	5S_rRNA links to Rfam database...	0.69	0.53	0.90	26	6992	3	1	2	0	23
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	33	5	23	5	28
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.66	1.00	21	3465	0	0	0	0	11

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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 McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

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