CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAalifold(20)		ProbKnot
MCC	0.762	>	0.679
Average MCC ± 95% Confidence Intervals	0.746 ± 0.094	>	0.685 ± 0.098
Sensitivity	0.669	<	0.700
Positive Predictive Value	0.872	>	0.664
Total TP	472	<	494
Total TN	75600	>	75397
Total FP	116	<	353
Total FP CONTRA	20	<	72
Total FP INCONS	49	<	178
Total FP COMP	47	<	103
Total FN	234	>	212
P-value	5.10776592382e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	472
Total TN	75600
Total FP	116
Total FP CONTRA	20
Total FP INCONS	49
Total FP COMP	47
Total FN	234

Total Scores
MCC	0.762
Average MCC ± 95% Confidence Intervals	0.746 ± 0.094
Sensitivity	0.669
Positive Predictive Value	0.872
Nr of predictions	24

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2. Individual counts for RNAalifold(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...	0.98	0.95	1.00	20	1109	1	0	0	1	1
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...	1.00	1.00	1.00	19	1138	2	0	0	2	0
3IZ4_A	tmRNA links to Rfam database...	0.65	0.48	0.87	46	25483	15	4	3	8	49
3IZF_C	5S_rRNA links to Rfam database...	0.90	0.89	0.91	31	2606	6	0	3	3	4
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	1	1	0	0	1
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...	0.86	0.74	1.00	25	2995	2	0	0	2	9
3NPB_A	SAM links to Rfam database...	0.75	0.57	1.00	21	2257	4	0	0	4	16
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.36	0.50	8	4748	9	3	5	1	14
3O58_2	5S_rRNA links to Rfam database...	0.97	0.94	1.00	29	2725	7	0	0	7	2
3PDR_A	ykoK links to Rfam database...	0.92	0.88	0.96	44	4794	3	1	1	1	6
3RKF_A	Purine links to Rfam database...	0.81	0.71	0.94	17	848	1	0	1	0	7
3SD1_A	THF links to Rfam database...	0.84	0.86	0.83	25	1503	5	4	1	0	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.46	0.41	0.52	12	5351	16	2	9	5	17
3ZEX_D	5S_rRNA links to Rfam database...	0.91	0.89	0.94	31	2763	6	0	2	4	4
4A1C_3	5S_rRNA links to Rfam database...	0.90	0.84	0.97	31	2731	1	0	1	0	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.19	5	4490	23	5	16	2	15
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
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...	0.63	0.40	1.00	6	490	0	0	0	0	9
4FRG_B	AdoCbl-variant links to Rfam database...	0.84	0.71	1.00	17	1185	0	0	0	0	7

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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 RNAalifold(20) - scored higher in this pairwise comparison

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

2. Individual counts for RNAalifold(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 ]