CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNASampler(20)		ProbKnot
MCC	0.721	>	0.679
Average MCC ± 95% Confidence Intervals	0.735 ± 0.094	>	0.685 ± 0.098
Sensitivity	0.625	<	0.700
Positive Predictive Value	0.837	>	0.664
Total TP	441	<	494
Total TN	75614	>	75397
Total FP	148	<	353
Total FP CONTRA	31	<	72
Total FP INCONS	55	<	178
Total FP COMP	62	<	103
Total FN	265	>	212
P-value	5.10776592382e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	441
Total TN	75614
Total FP	148
Total FP CONTRA	31
Total FP INCONS	55
Total FP COMP	62
Total FN	265

Total Scores
MCC	0.721
Average MCC ± 95% Confidence Intervals	0.735 ± 0.094
Sensitivity	0.625
Positive Predictive Value	0.837
Nr of predictions	24

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2. Individual counts for RNASampler(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...	0.94	0.94	0.94	17	339	2	0	1	1	1
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	4	1831	2	0	0	2	7
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.34	0.11	1.00	4	2041	0	0	0	0	31
3AMU_B	tRNA links to Rfam database...	0.95	0.95	0.95	18	1138	4	0	1	3	1
3IZ4_A	tmRNA links to Rfam database...	0.52	0.41	0.65	39	25476	26	15	6	5	56
3IZF_C	5S_rRNA links to Rfam database...	0.92	0.86	1.00	30	2610	2	0	0	2	5
3J20_0	tRNA links to Rfam database...	0.90	0.90	0.90	19	1198	3	1	1	1	2
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.50	0.63	17	2993	12	3	7	2	17
3NPB_A	SAM links to Rfam database...	0.75	0.57	1.00	21	2257	5	0	0	5	16
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.50	0.52	11	4743	19	5	5	9	11
3O58_2	5S_rRNA links to Rfam database...	0.93	0.87	1.00	27	2727	5	0	0	5	4
3PDR_A	ykoK links to Rfam database...	0.84	0.76	0.93	38	4799	5	1	2	2	12
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.81	0.69	0.95	20	1512	1	0	1	0	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.35	0.31	0.39	9	5351	21	3	11	7	20
3ZEX_D	5S_rRNA links to Rfam database...	0.83	0.69	1.00	24	2772	1	0	0	1	11
4A1C_3	5S_rRNA links to Rfam database...	0.90	0.81	1.00	30	2733	0	0	0	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	30	3	13	14	15
4AOB_A	SAM links to Rfam database...	0.70	0.59	0.85	17	1417	4	0	3	1	12
4ENB_A	crcB links to Rfam database...	0.68	0.47	1.00	7	465	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	0	0	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.64	0.54	0.76	13	1185	4	0	4	0	11

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Performance of ProbKnot - scored lower 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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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 RNASampler(20) - scored higher in this pairwise comparison

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

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

Performance of ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

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