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)		RSpredict(20)
MCC	0.607	>	0.559
Average MCC ± 95% Confidence Intervals	0.581 ± 0.094	>	0.566 ± 0.099
Sensitivity	0.405	<	0.446
Positive Predictive Value	0.915	>	0.705
Total TP	375	<	413
Total TN	191614	>	191438
Total FP	56	<	207
Total FP CONTRA	7	<	42
Total FP INCONS	28	<	131
Total FP COMP	21	<	34
Total FN	552	>	514
P-value	5.19332990918e-08

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Performance plots

Comparison of performance of Carnac(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 Carnac(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 Carnac(20) and RSpredict(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Carnac(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 Carnac(20) and RSpredict(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	375
Total TN	191614
Total FP	56
Total FP CONTRA	7
Total FP INCONS	28
Total FP COMP	21
Total FN	552

Total Scores
MCC	0.607
Average MCC ± 95% Confidence Intervals	0.581 ± 0.094
Sensitivity	0.405
Positive Predictive Value	0.915
Nr of predictions	24

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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
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
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
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.15	0.71	5	11774	3	0	2	1	28
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

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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	413
Total TN	191438
Total FP	207
Total FP CONTRA	42
Total FP INCONS	131
Total FP COMP	34
Total FN	514

Total Scores
MCC	0.559
Average MCC ± 95% Confidence Intervals	0.566 ± 0.099
Sensitivity	0.446
Positive Predictive Value	0.705
Nr of predictions	24

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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
2KDQ_B	mir-TAR links to Rfam database...	0.85	0.73	1.00	8	398	0	0	0	0	3
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	11	5	3	3	7
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
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...	0.61	0.41	0.92	11	2991	1	0	1	0	16
3GX2_A	SAM links to Rfam database...	0.33	0.15	0.75	6	4363	2	0	2	0	34
3IVN_B	Purine links to Rfam database...	0.78	0.65	0.95	20	2325	1	0	1	0	11
3IZ4_A	tmRNA links to Rfam database...	0.53	0.43	0.65	57	70788	35	8	23	4	75
3IZF_C	5S_rRNA links to Rfam database...	0.75	0.61	0.92	33	6867	3	1	2	0	21
3JYV_7	tRNA links to Rfam database...	0.77	0.63	0.95	20	2829	1	0	1	0	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.28	0.27	0.30	9	12216	33	5	16	12	24
3JYX_3	5S_rRNA links to Rfam database...	0.61	0.56	0.68	15	6306	13	0	7	6	12
3LA5_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2465	0	0	0	0	14
3NPB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	7015	6	1	5	0	46
3O58_2	5S_rRNA links to Rfam database...	0.76	0.76	0.76	29	7222	10	3	6	1	9
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.34	0.30	12	12363	28	12	16	0	23
3PDR_A	ykoK links to Rfam database...	0.67	0.49	0.92	35	12842	5	0	3	2	37
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.68	0.60	0.78	25	3884	7	1	6	0	17
4A1C_3	5S_rRNA links to Rfam database...	0.48	0.33	0.69	18	7114	8	0	8	0	36
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.18	0.20	6	11751	30	6	18	6	27
4AOB_A	SAM links to Rfam database...	0.28	0.14	0.55	6	4360	5	0	5	0	36
4ENB_A	crcB links to Rfam database...	0.48	0.32	0.75	6	1267	2	0	2	0	13
4ENC_A	crcB links to Rfam database...	0.45	0.32	0.67	6	1317	3	0	3	0	13

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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 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 ]