CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	UNAFold		RNASampler(seed)
MCC	0.740	>	0.728
Average MCC ± 95% Confidence Intervals	0.771 ± 0.158	>	0.736 ± 0.126
Sensitivity	0.767	>	0.634
Positive Predictive Value	0.721	<	0.843
Total TP	312	>	258
Total TN	30671	<	30798
Total FP	188	>	77
Total FP CONTRA	42	>	17
Total FP INCONS	79	>	31
Total FP COMP	67	>	29
Total FN	95	<	149
P-value	1.23248012054e-07

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Performance plots

Comparison of performance of UNAFold and RNASampler(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 UNAFold and RNASampler(seed)).
Comparison of performance of UNAFold and RNASampler(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 UNAFold and RNASampler(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 UNAFold and RNASampler(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 UNAFold and RNASampler(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for UNAFold and RNASampler(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 UNAFold and RNASampler(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for UNAFold and RNASampler(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 UNAFold and RNASampler(seed)).

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Performance of UNAFold - scored higher in this pairwise comparison

1. Total counts & total scores for UNAFold

Total Base Pair Counts
Total TP	312
Total TN	30671
Total FP	188
Total FP CONTRA	42
Total FP INCONS	79
Total FP COMP	67
Total FN	95

Total Scores
MCC	0.740
Average MCC ± 95% Confidence Intervals	0.771 ± 0.158
Sensitivity	0.767
Positive Predictive Value	0.721
Nr of predictions	19

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2. Individual counts for UNAFold [ 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...	1.00	1.00	1.00	10	164	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	449	1	0	0	1	0
2KUR_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	448	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	429	1	0	0	1	0
2KUV_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	420	0	0	0	0	0
2KUW_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	452	1	0	0	1	0
2L1F_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	31	10	2	19	2
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.50	0.35	11	4733	34	5	15	14	11
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...	0.77	0.76	0.79	22	1505	6	4	2	0	7
3W3S_B	tRNA-Sec links to Rfam database...	0.61	0.61	0.63	20	1957	13	4	8	1	13
3ZEX_C	5_8S_rRNA links to Rfam database...	0.30	0.34	0.26	10	5336	43	5	23	15	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	42	11	17	14	15

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Performance of RNASampler(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	258
Total TN	30798
Total FP	77
Total FP CONTRA	17
Total FP INCONS	31
Total FP COMP	29
Total FN	149

Total Scores
MCC	0.728
Average MCC ± 95% Confidence Intervals	0.736 ± 0.126
Sensitivity	0.634
Positive Predictive Value	0.843
Nr of predictions	19

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2. Individual counts for RNASampler(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...	1.00	1.00	1.00	10	164	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	0.94	0.89	1.00	16	451	1	0	0	1	2
2KUR_A	K10_TLS links to Rfam database...	0.94	0.89	1.00	17	450	0	0	0	0	2
2KUU_A	K10_TLS links to Rfam database...	0.94	0.89	1.00	16	431	1	0	0	1	2
2KUV_A	K10_TLS links to Rfam database...	0.94	0.89	1.00	17	422	0	0	0	0	2
2KUW_A	K10_TLS links to Rfam database...	0.94	0.89	1.00	16	454	1	0	0	1	2
2L1F_A	Gammaretro_CES links to Rfam database...	0.83	0.70	1.00	16	747	0	0	0	0	7
2L1F_B	Gammaretro_CES links to Rfam database...	0.84	0.71	1.00	17	774	0	0	0	0	7
2L94_A	HIV_FE links to Rfam database...	0.70	0.56	0.91	10	346	2	0	1	1	8
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	518	10	0	10	0	18
3A3A_A	tRNA-Sec links to Rfam database...	0.77	0.60	1.00	18	1482	0	0	0	0	12
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3JYX_4	5_8S_rRNA links to Rfam database...	0.70	0.83	0.59	10	4739	13	6	1	6	2
3O58_3	5_8S_rRNA links to Rfam database...	0.54	0.50	0.58	11	4745	13	5	3	5	11
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...	0.72	0.55	0.94	16	1516	1	0	1	0	13
3W3S_B	tRNA-Sec links to Rfam database...	0.60	0.36	1.00	12	1977	1	0	0	1	21
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.31	0.50	9	5356	14	2	7	5	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.40	0.40	0.40	8	4496	20	4	8	8	12

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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 UNAFold - scored higher in this pairwise comparison

1. Total counts & total scores for UNAFold

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

Performance of RNASampler(seed) - scored lower in this pairwise comparison

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

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