CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Murlet(20)		RSpredict(seed)
MCC	0.582	>	0.249
Average MCC ± 95% Confidence Intervals	0.586 ± 0.067	>	0.217 ± 0.109
Sensitivity	0.425	>	0.110
Positive Predictive Value	0.800	>	0.569
Total TP	429	>	111
Total TN	202189	<	202530
Total FP	138	>	88
Total FP CONTRA	13	>	6
Total FP INCONS	94	>	78
Total FP COMP	31	>	4
Total FN	580	<	898
P-value	5.1503931209e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	429
Total TN	202189
Total FP	138
Total FP CONTRA	13
Total FP INCONS	94
Total FP COMP	31
Total FN	580

Total Scores
MCC	0.582
Average MCC ± 95% Confidence Intervals	0.586 ± 0.067
Sensitivity	0.425
Positive Predictive Value	0.800
Nr of predictions	27

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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
2L94_A	HIV_FE links to Rfam database...	0.53	0.50	0.59	10	973	7	0	7	0	10
2WRQ_Y	tRNA links to Rfam database...	0.41	0.41	0.41	7	2833	12	6	4	2	10
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...	0.80	0.70	0.90	19	2829	2	0	2	0	8
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.41	0.17	1.00	7	5144	0	0	0	0	35
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
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
3JYV_7	tRNA links to Rfam database...	0.67	0.53	0.85	17	2830	3	0	3	0	15
3JYX_3	5S_rRNA links to Rfam database...	0.60	0.52	0.70	14	6308	11	0	6	5	13
3JYX_4	5_8S_rRNA links to Rfam database...	0.36	0.27	0.47	9	12227	15	0	10	5	24
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
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

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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	111
Total TN	202530
Total FP	88
Total FP CONTRA	6
Total FP INCONS	78
Total FP COMP	4
Total FN	898

Total Scores
MCC	0.249
Average MCC ± 95% Confidence Intervals	0.217 ± 0.109
Sensitivity	0.110
Positive Predictive Value	0.569
Nr of predictions	27

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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
2KDQ_B	mir-TAR links to Rfam database...	0.85	0.73	1.00	8	398	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.57	0.50	0.67	10	975	5	0	5	0	10
2WRQ_Y	tRNA links to Rfam database...	0.00	0.00	0.00	0	2848	3	1	1	1	17
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.28	0.20	0.40	4	4550	8	2	4	2	16
2XQD_Y	tRNA links to Rfam database...	0.00	0.00	0.00	0	2845	5	0	5	0	27
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.34	0.17	0.70	7	5141	3	0	3	0	35
3A2K_C	tRNA links to Rfam database...	0.00	0.00	0.00	0	2924	2	0	2	0	28
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3001	2	0	2	0	27
3GX2_A	SAM links to Rfam database...	0.36	0.15	0.86	6	4364	1	0	1	0	34
3IVN_B	Purine links to Rfam database...	0.69	0.52	0.94	16	2329	1	0	1	0	15
3IZ4_A	tmRNA links to Rfam database...	0.21	0.08	0.59	10	70859	7	0	7	0	122
3IZF_C	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6898	5	0	5	0	54
3JYV_7	tRNA links to Rfam database...	0.00	0.00	0.00	0	2846	4	0	4	0	32
3JYX_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6323	5	1	4	0	27
3JYX_4	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12241	5	0	5	0	33
3LA5_A	Purine links to Rfam database...	0.70	0.50	1.00	17	2468	0	0	0	0	17
3NPB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	7017	4	0	4	0	46
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7257	3	0	3	0	38
3O58_3	5_8S_rRNA links to Rfam database...	0.23	0.09	0.60	3	12398	2	0	2	0	32
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	12872	8	0	8	0	72
3RKF_A	Purine links to Rfam database...	0.71	0.53	0.95	18	2192	1	0	1	0	16
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11777	5	1	3	1	33
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7136	4	1	3	0	54
4AOB_A	SAM links to Rfam database...	0.35	0.14	0.86	6	4364	1	0	1	0	36
4ENB_A	crcB links to Rfam database...	0.30	0.16	0.60	3	1270	2	0	2	0	16
4ENC_A	crcB links to Rfam database...	0.30	0.16	0.60	3	1321	2	0	2	0	16

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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 Murlet(20) - scored higher in this pairwise comparison

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

2. Individual counts for Murlet(20) [ 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 ]