CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Carnac(20)		Murlet(20)
MCC	0.590	>	0.590
Average MCC ± 95% Confidence Intervals	0.566 ± 0.072	<	0.587 ± 0.059
Sensitivity	0.389	<	0.438
Positive Predictive Value	0.899	>	0.799
Total TP	585	<	658
Total TN	284056	>	283883
Total FP	92	<	210
Total FP CONTRA	9	<	17
Total FP INCONS	57	<	149
Total FP COMP	26	<	44
Total FN	919	>	846
P-value	0.339915559821

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Performance plots

Comparison of performance of Carnac(20) and Murlet(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 Carnac(20) and Murlet(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 Carnac(20) and Murlet(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Carnac(20) and Murlet(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 Carnac(20) and Murlet(20)).

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

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

Total Base Pair Counts
Total TP	585
Total TN	284056
Total FP	92
Total FP CONTRA	9
Total FP INCONS	57
Total FP COMP	26
Total FN	919

Total Scores
MCC	0.590
Average MCC ± 95% Confidence Intervals	0.566 ± 0.072
Sensitivity	0.389
Positive Predictive Value	0.899
Nr of predictions	38

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2. Individual counts for Carnac(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...	0.73	0.55	1.00	6	400	0	0	0	0	5
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2XQD_Y	tRNA links to Rfam database...	0.79	0.63	1.00	17	2833	0	0	0	0	10
3A2K_C	tRNA links to Rfam database...	0.78	0.61	1.00	17	2909	0	0	0	0	11
3AMU_B	tRNA links to Rfam database...	0.69	0.59	0.80	16	2983	6	0	4	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.50	0.28	0.89	16	7363	2	1	1	0	41
3GX2_A	SAM links to Rfam database...	0.57	0.33	1.00	13	4358	0	0	0	0	27
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...	0.47	0.23	0.94	31	70843	2	0	2	0	101
3IZF_C	5S_rRNA links to Rfam database...	0.73	0.56	0.97	30	6872	1	0	1	0	24
3J20_0	tRNA links to Rfam database...	0.62	0.53	0.73	16	2828	7	0	6	1	14
3J20_1	tRNA links to Rfam database...	0.86	0.74	1.00	17	2909	0	0	0	0	6
3J2L_3	5S_rRNA links to Rfam database...	0.46	0.34	0.64	18	7847	11	0	10	1	35
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_7	5S_rRNA links to Rfam database...	0.65	0.44	0.96	24	7115	1	0	1	0	30
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7503	0	0	0	0	33
3J3F_7	5S_rRNA links to Rfam database...	0.66	0.44	1.00	22	7238	0	0	0	0	28
3J3F_8	5_8S_rRNA links to Rfam database...	0.50	0.25	1.00	9	12237	0	0	0	0	27
3J3V_B	5S_rRNA links to Rfam database...	0.58	0.35	0.95	20	7000	1	0	1	0	37
3JYV_7	tRNA links to Rfam database...	0.68	0.50	0.94	16	2833	1	0	1	0	16
3JYX_4	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	12239	2	0	0	2	26
3JYX_3	5S_rRNA links to Rfam database...	0.64	0.56	0.75	15	6308	10	1	4	5	12
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...	0.44	0.20	1.00	9	7012	2	0	0	2	37
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...	0.51	0.26	1.00	9	12394	0	0	0	0	26
3PDR_A	ykoK links to Rfam database...	0.62	0.40	0.97	29	12850	3	0	1	2	43
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...	0.60	0.38	0.94	16	3899	1	0	1	0	26
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.53	1.00	26	6995	0	0	0	0	23
3ZEX_C	5_8S_rRNA links to Rfam database...	0.31	0.13	0.70	7	14186	3	1	2	0	45
3ZND_W	tRNA links to Rfam database...	0.47	0.39	0.56	9	2987	10	0	7	3	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.15	0.71	5	11774	3	0	2	1	28
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4AOB_A	SAM links to Rfam database...	0.49	0.33	0.74	14	4352	6	1	4	1	28
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19
4FRG_B	AdoCbl-variant links to Rfam database...	0.43	0.19	1.00	6	3480	0	0	0	0	26

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Performance of Murlet(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	658
Total TN	283883
Total FP	210
Total FP CONTRA	17
Total FP INCONS	149
Total FP COMP	44
Total FN	846

Total Scores
MCC	0.590
Average MCC ± 95% Confidence Intervals	0.587 ± 0.059
Sensitivity	0.438
Positive Predictive Value	0.799
Nr of predictions	38

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2. Individual counts for Murlet(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...	0.67	0.45	1.00	5	401	0	0	0	0	6
2WRQ_Y	tRNA links to Rfam database...	0.41	0.41	0.41	7	2833	12	6	4	2	10
2XQD_Y	tRNA links to Rfam database...	0.80	0.70	0.90	19	2829	2	0	2	0	8
3A2K_C	tRNA links to Rfam database...	0.78	0.68	0.90	19	2905	2	0	2	0	9
3AMU_B	tRNA links to Rfam database...	0.77	0.67	0.90	18	2983	3	0	2	1	9
3G4S_9	5S_rRNA links to Rfam database...	0.58	0.39	0.88	22	7356	3	1	2	0	35
3GX2_A	SAM links to Rfam database...	0.61	0.38	1.00	15	4356	1	0	0	1	25
3IVN_B	Purine links to Rfam database...	0.69	0.48	1.00	15	2331	0	0	0	0	16
3IZ4_A	tmRNA links to Rfam database...	0.40	0.24	0.65	32	70827	21	1	16	4	100
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.56	0.91	30	6870	4	0	3	1	24
3J20_0	tRNA links to Rfam database...	0.58	0.47	0.74	14	2831	5	0	5	0	16
3J20_1	tRNA links to Rfam database...	0.68	0.57	0.81	13	2910	3	0	3	0	10
3J2L_3	5S_rRNA links to Rfam database...	0.69	0.49	0.96	26	7848	3	0	1	2	27
3J3D_C	tRNA links to Rfam database...	0.78	0.64	0.95	18	2756	1	0	1	0	10
3J3E_7	5S_rRNA links to Rfam database...	0.77	0.63	0.94	34	7104	2	0	2	0	20
3J3E_8	5_8S_rRNA links to Rfam database...	0.24	0.15	0.38	5	7490	13	1	7	5	28
3J3F_7	5S_rRNA links to Rfam database...	0.69	0.50	0.96	25	7234	1	0	1	0	25
3J3F_8	5_8S_rRNA links to Rfam database...	0.48	0.36	0.65	13	12226	10	0	7	3	23
3J3V_B	5S_rRNA links to Rfam database...	0.63	0.40	1.00	23	6998	0	0	0	0	34
3JYV_7	tRNA links to Rfam database...	0.67	0.53	0.85	17	2830	3	0	3	0	15
3JYX_4	5_8S_rRNA links to Rfam database...	0.36	0.27	0.47	9	12227	15	0	10	5	24
3JYX_3	5S_rRNA links to Rfam database...	0.60	0.52	0.70	14	6308	11	0	6	5	13
3LA5_A	Purine links to Rfam database...	0.68	0.47	1.00	16	2469	0	0	0	0	18
3NPB_A	SAM links to Rfam database...	0.55	0.35	0.89	16	7003	2	1	1	0	30
3O58_2	5S_rRNA links to Rfam database...	0.89	0.82	0.97	31	7228	2	0	1	1	7
3O58_3	5_8S_rRNA links to Rfam database...	0.33	0.23	0.47	8	12386	12	2	7	3	27
3PDR_A	ykoK links to Rfam database...	0.70	0.53	0.93	38	12839	3	0	3	0	34
3RKF_A	Purine links to Rfam database...	0.68	0.47	1.00	16	2195	0	0	0	0	18
3SD1_A	THF links to Rfam database...	0.68	0.57	0.83	24	3887	5	1	4	0	18
3ZEX_D	5S_rRNA links to Rfam database...	0.77	0.65	0.91	32	6986	3	0	3	0	17
3ZEX_C	5_8S_rRNA links to Rfam database...	0.34	0.23	0.50	12	14172	15	1	11	3	40
3ZND_W	tRNA links to Rfam database...	0.45	0.39	0.53	9	2986	11	0	8	3	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.20	5	11756	24	2	18	4	28
4A1C_3	5S_rRNA links to Rfam database...	0.59	0.41	0.85	22	7114	4	0	4	0	32
4AOB_A	SAM links to Rfam database...	0.72	0.55	0.96	23	4347	2	0	1	1	19
4ENB_A	crcB links to Rfam database...	0.46	0.21	1.00	4	1271	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.51	0.26	1.00	5	1321	0	0	0	0	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.17	0.13	0.25	4	3470	12	1	11	0	28

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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 Carnac(20) - scored higher in this pairwise comparison

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

2. Individual counts for Carnac(20) [ download as .csv ]

Performance of Murlet(20) - scored lower in this pairwise comparison

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

2. Individual counts for Murlet(20) [ download as .csv ]