CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAshapes		PPfold(seed)
MCC	0.633	>	0.094
Average MCC ± 95% Confidence Intervals	0.632 ± 0.110	>	0.039 ± 0.056
Sensitivity	0.638	>	0.019
Positive Predictive Value	0.637	>	0.474
Total TP	298	>	9
Total TN	34312	<	34761
Total FP	223	>	49
Total FP CONTRA	38	>	0
Total FP INCONS	132	>	10
Total FP COMP	53	>	39
Total FN	169	<	458
P-value	2.89169006118e-08

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Performance plots

Comparison of performance of RNAshapes and PPfold(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 RNAshapes and PPfold(seed)).
Comparison of performance of RNAshapes and PPfold(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 RNAshapes and PPfold(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 RNAshapes and PPfold(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 RNAshapes and PPfold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAshapes and PPfold(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 RNAshapes and PPfold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAshapes and PPfold(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 RNAshapes and PPfold(seed)).

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Performance of RNAshapes - scored higher in this pairwise comparison

1. Total counts & total scores for RNAshapes

Total Base Pair Counts
Total TP	298
Total TN	34312
Total FP	223
Total FP CONTRA	38
Total FP INCONS	132
Total FP COMP	53
Total FN	169

Total Scores
MCC	0.633
Average MCC ± 95% Confidence Intervals	0.632 ± 0.110
Sensitivity	0.638
Positive Predictive Value	0.637
Nr of predictions	19

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	0	5	0	7
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3J16_L	tRNA links to Rfam database...	0.59	0.57	0.63	12	1140	7	0	7	0	9
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
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...	0.77	0.79	0.75	27	2984	14	1	8	5	7
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
3UZL_B	tRNA links to Rfam database...	0.43	0.50	0.38	8	1272	17	4	9	4	8
3W3S_B	tRNA-Sec links to Rfam database...	0.60	0.58	0.63	19	1959	12	2	9	1	14
3ZEX_C	5_8S_rRNA links to Rfam database...	0.29	0.34	0.26	10	5335	42	5	24	13	19
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.80	0.93	28	2766	6	0	2	4	7
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	7	0	4	3	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	11	16	14	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...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.59	0.57	0.62	16	1822	10	2	8	0	12

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

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

Total Base Pair Counts
Total TP	9
Total TN	34761
Total FP	49
Total FP CONTRA	0
Total FP INCONS	10
Total FP COMP	39
Total FN	458

Total Scores
MCC	0.094
Average MCC ± 95% Confidence Intervals	0.039 ± 0.056
Sensitivity	0.019
Positive Predictive Value	0.474
Nr of predictions	19

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.49	0.33	0.75	6	520	2	0	2	0	12
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	1157	0	0	0	0	19
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	1159	0	0	0	0	21
3J20_0	tRNA links to Rfam database...	0.00	0.00	0.00	0	1219	0	0	0	0	21
3J20_1	tRNA links to Rfam database...	0.00	0.00	0.00	0	1112	0	0	0	0	20
3J2L_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	3020	0	0	0	0	34
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	866	0	0	0	0	24
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
3UZL_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	1293	0	0	0	0	16
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	1989	0	0	0	0	33
3ZEX_C	5_8S_rRNA links to Rfam database...	0.15	0.07	0.33	2	5368	24	0	4	20	27
3ZEX_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2796	0	0	0	0	35
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2763	0	0	0	0	37
4A1C_2	5_8S_rRNA links to Rfam database...	0.10	0.05	0.20	1	4511	23	0	4	19	19
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	1437	0	0	0	0	29
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	472	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	496	0	0	0	0	15
4FRG_B	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	1202	0	0	0	0	24
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	1848	0	0	0	0	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 RNAshapes - scored higher in this pairwise comparison

1. Total counts & total scores for RNAshapes

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

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

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

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