CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ProbKnot		Murlet(20)
MCC	0.679	>	0.667
Average MCC ± 95% Confidence Intervals	0.685 ± 0.098	>	0.656 ± 0.096
Sensitivity	0.700	>	0.567
Positive Predictive Value	0.664	<	0.792
Total TP	494	>	400
Total TN	75397	<	75636
Total FP	353	>	148
Total FP CONTRA	72	>	21
Total FP INCONS	178	>	84
Total FP COMP	103	>	43
Total FN	212	<	306
P-value	5.6410608252e-08

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Performance plots

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

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Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	494
Total TN	75397
Total FP	353
Total FP CONTRA	72
Total FP INCONS	178
Total FP COMP	103
Total FN	212

Total Scores
MCC	0.679
Average MCC ± 95% Confidence Intervals	0.685 ± 0.098
Sensitivity	0.700
Positive Predictive Value	0.664
Nr of predictions	24

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	26	0	6	20	3
2XQD_Y	tRNA links to Rfam database...	1.00	1.00	1.00	21	1108	2	0	0	2	0
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.25	0.26	0.26	9	2011	26	1	24	1	26
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	9	0	5	4	4
3IZ4_A	tmRNA links to Rfam database...	0.59	0.61	0.57	58	25435	49	17	26	6	37
3IZF_C	5S_rRNA links to Rfam database...	0.90	0.91	0.89	32	2604	7	0	4	3	3
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	8	0	5	3	5
3J2L_3	5S_rRNA links to Rfam database...	0.79	0.76	0.81	26	2988	11	0	6	5	8
3NPB_A	SAM links to Rfam database...	0.79	0.73	0.87	27	2247	9	0	4	5	10
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.50	0.29	11	4726	42	10	17	15	11
3O58_2	5S_rRNA links to Rfam database...	0.91	0.94	0.88	29	2721	10	0	4	6	2
3PDR_A	ykoK links to Rfam database...	0.88	0.92	0.85	46	4786	10	5	3	2	4
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.66	0.69	0.65	20	1502	11	6	5	0	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.48	0.52	0.45	15	5341	22	4	14	4	14
3ZEX_D	5S_rRNA links to Rfam database...	0.90	0.86	0.94	30	2764	7	0	2	5	5
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	7	0	4	3	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.25	0.13	5	4477	49	13	21	15	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	1	1	0	0	4
4ENC_A	crcB links to Rfam database...	0.52	0.53	0.53	8	481	8	0	7	1	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.38	0.38	0.41	9	1180	13	6	7	0	15

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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	400
Total TN	75636
Total FP	148
Total FP CONTRA	21
Total FP INCONS	84
Total FP COMP	43
Total FN	306

Total Scores
MCC	0.667
Average MCC ± 95% Confidence Intervals	0.656 ± 0.096
Sensitivity	0.567
Positive Predictive Value	0.792
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
2L94_A	HIV_FE links to Rfam database...	0.51	0.50	0.56	9	341	8	0	7	1	9
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	4	1831	3	0	0	3	7
2XQD_Y	tRNA links to Rfam database...	0.88	0.86	0.90	18	1109	3	0	2	1	3
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.44	0.20	1.00	7	2038	0	0	0	0	28
3AMU_B	tRNA links to Rfam database...	0.89	0.89	0.89	17	1138	4	0	2	2	2
3IZ4_A	tmRNA links to Rfam database...	0.46	0.33	0.66	31	25489	22	3	13	6	64
3IZF_C	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2609	5	0	2	3	6
3J20_0	tRNA links to Rfam database...	0.65	0.62	0.68	13	1200	6	1	5	0	8
3J20_1	tRNA links to Rfam database...	0.69	0.60	0.80	12	1097	4	0	3	1	8
3J2L_3	5S_rRNA links to Rfam database...	0.84	0.74	0.96	25	2994	4	0	1	3	9
3NPB_A	SAM links to Rfam database...	0.65	0.43	1.00	16	2262	2	0	0	2	21
3O58_3	5_8S_rRNA links to Rfam database...	0.37	0.32	0.44	7	4748	13	4	5	4	15
3O58_2	5S_rRNA links to Rfam database...	1.00	1.00	1.00	31	2723	2	0	0	2	0
3PDR_A	ykoK links to Rfam database...	0.84	0.76	0.93	38	4799	3	1	2	0	12
3RKF_A	Purine links to Rfam database...	0.81	0.67	1.00	16	850	0	0	0	0	8
3SD1_A	THF links to Rfam database...	0.82	0.83	0.83	24	1504	5	4	1	0	5
3ZEX_C	5_8S_rRNA links to Rfam database...	0.42	0.38	0.48	11	5351	16	2	10	4	18
3ZEX_D	5S_rRNA links to Rfam database...	0.90	0.86	0.94	30	2764	5	0	2	3	5
4A1C_3	5S_rRNA links to Rfam database...	0.72	0.59	0.88	22	2738	4	0	3	1	15
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.20	5	4491	24	5	15	4	15
4AOB_A	SAM links to Rfam database...	0.87	0.76	1.00	22	1415	3	0	0	3	7
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.57	0.33	1.00	5	491	0	0	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.19	0.17	0.25	4	1186	12	1	11	0	20

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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 ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

2. Individual counts for ProbKnot [ 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 ]