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(seed)		RNAalifold(20)
MCC	0.541	>	0.493
Average MCC ± 95% Confidence Intervals	0.585 ± 0.177	>	0.508 ± 0.148
Sensitivity	0.399	>	0.385
Positive Predictive Value	0.739	>	0.636
Total TP	116	>	112
Total TN	60338	>	60319
Total FP	60	<	74
Total FP CONTRA	5	<	7
Total FP INCONS	36	<	57
Total FP COMP	19	>	10
Total FN	175	<	179
P-value	0.0

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	116
Total TN	60338
Total FP	60
Total FP CONTRA	5
Total FP INCONS	36
Total FP COMP	19
Total FN	175

Total Scores
MCC	0.541
Average MCC ± 95% Confidence Intervals	0.585 ± 0.177
Sensitivity	0.399
Positive Predictive Value	0.739
Nr of predictions	9

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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...	0.95	0.91	1.00	10	396	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.71	0.55	0.92	11	978	1	0	1	0	9
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.30	0.50	10	12226	13	2	8	3	23
3O58_3	5_8S_rRNA links to Rfam database...	0.45	0.34	0.60	12	12383	12	2	6	4	23
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.60	0.38	0.94	16	3899	1	0	1	0	26
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.19	0.53	10	14177	13	1	8	4	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.31	0.24	0.40	8	11761	20	0	12	8	25

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

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

Total Base Pair Counts
Total TP	112
Total TN	60319
Total FP	74
Total FP CONTRA	7
Total FP INCONS	57
Total FP COMP	10
Total FN	179

Total Scores
MCC	0.493
Average MCC ± 95% Confidence Intervals	0.508 ± 0.148
Sensitivity	0.385
Positive Predictive Value	0.636
Nr of predictions	9

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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
2KDQ_B	mir-TAR links to Rfam database...	0.60	0.36	1.00	4	402	0	0	0	0	7
2L94_A	HIV_FE links to Rfam database...	0.53	0.50	0.59	10	973	7	0	7	0	10
3IVN_B	Purine links to Rfam database...	0.74	0.58	0.95	18	2327	1	1	0	0	13
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.30	0.50	10	12226	15	0	10	5	23
3O58_3	5_8S_rRNA links to Rfam database...	0.37	0.26	0.53	9	12386	8	2	6	0	26
3RKF_A	Purine links to Rfam database...	0.68	0.50	0.94	17	2193	1	0	1	0	17
3SD1_A	THF links to Rfam database...	0.70	0.60	0.83	25	3886	5	1	4	0	17
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.27	0.56	14	14171	14	1	10	3	38
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	23	2	19	2	28

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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(seed) - scored higher in this pairwise comparison

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

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

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

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

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