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)		Pknots
MCC	0.618	>	0.540
Average MCC ± 95% Confidence Intervals	0.609 ± 0.071	>	0.592 ± 0.111
Sensitivity	0.467	<	0.487
Positive Predictive Value	0.822	>	0.605
Total TP	398	<	415
Total TN	128045	>	127843
Total FP	110	<	307
Total FP CONTRA	13	<	50
Total FP INCONS	73	<	221
Total FP COMP	24	<	36
Total FN	454	>	437
P-value	5.10776592382e-08

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Performance plots

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

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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	398
Total TN	128045
Total FP	110
Total FP CONTRA	13
Total FP INCONS	73
Total FP COMP	24
Total FN	454

Total Scores
MCC	0.618
Average MCC ± 95% Confidence Intervals	0.609 ± 0.071
Sensitivity	0.467
Positive Predictive Value	0.822
Nr of predictions	24

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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
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_3	5S_rRNA links to Rfam database...	0.59	0.41	0.85	22	7114	4	0	4	0	32
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.20	5	11756	24	2	18	4	28
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 Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	415
Total TN	127843
Total FP	307
Total FP CONTRA	50
Total FP INCONS	221
Total FP COMP	36
Total FN	437

Total Scores
MCC	0.540
Average MCC ± 95% Confidence Intervals	0.592 ± 0.111
Sensitivity	0.487
Positive Predictive Value	0.605
Nr of predictions	24

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2. Individual counts for Pknots [ 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
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	12	5	3	4	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...	0.45	0.43	0.48	12	2901	13	2	11	0	16
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...	0.25	0.21	0.31	12	7342	27	0	27	0	45
3GX2_A	SAM links to Rfam database...	0.47	0.40	0.55	16	4342	14	1	12	1	24
3IVN_B	Purine links to Rfam database...	0.78	0.65	0.95	20	2325	1	0	1	0	11
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.61	0.80	33	6862	8	1	7	0	21
3JYV_7	tRNA links to Rfam database...	0.81	0.66	1.00	21	2829	0	0	0	0	11
3JYX_3	5S_rRNA links to Rfam database...	0.34	0.37	0.31	10	6296	24	9	13	2	17
3JYX_4	5_8S_rRNA links to Rfam database...	0.18	0.21	0.16	7	12203	41	13	23	5	26
3LA5_A	Purine links to Rfam database...	0.80	0.65	1.00	22	2463	0	0	0	0	12
3NPB_A	SAM links to Rfam database...	0.76	0.67	0.86	31	6985	8	1	4	3	15
3O58_2	5S_rRNA links to Rfam database...	0.83	0.74	0.93	28	7230	3	0	2	1	10
3O58_3	5_8S_rRNA links to Rfam database...	0.27	0.31	0.24	11	12357	38	11	24	3	24
3PDR_A	ykoK links to Rfam database...	0.54	0.44	0.65	32	12831	19	0	17	2	40
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...	0.65	0.52	0.81	22	3889	5	0	5	0	20
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...	0.24	0.24	0.25	8	11749	36	3	21	12	25
4AOB_A	SAM links to Rfam database...	0.17	0.14	0.21	6	4343	23	1	21	1	36
4ENB_A	crcB links to Rfam database...	0.83	0.79	0.88	15	1258	2	1	1	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

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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 Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

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