CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNASLOpt		Carnac(20)
MCC	0.540	>	0.524
Average MCC ± 95% Confidence Intervals	0.575 ± 0.157	>	0.445 ± 0.186
Sensitivity	0.443	>	0.337
Positive Predictive Value	0.664	<	0.820
Total TP	180	>	137
Total TN	63976	<	64080
Total FP	113	>	34
Total FP CONTRA	15	>	2
Total FP INCONS	76	>	28
Total FP COMP	22	>	4
Total FN	226	<	269
P-value	9.81657399344e-06

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Performance plots

Comparison of performance of RNASLOpt and Carnac(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 RNASLOpt and Carnac(20)).
Comparison of performance of RNASLOpt and Carnac(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 RNASLOpt and Carnac(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 RNASLOpt and Carnac(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 RNASLOpt and Carnac(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASLOpt and Carnac(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 RNASLOpt and Carnac(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASLOpt and Carnac(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 RNASLOpt and Carnac(20)).

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Performance of RNASLOpt - scored higher in this pairwise comparison

1. Total counts & total scores for RNASLOpt

Total Base Pair Counts
Total TP	180
Total TN	63976
Total FP	113
Total FP CONTRA	15
Total FP INCONS	76
Total FP COMP	22
Total FN	226

Total Scores
MCC	0.540
Average MCC ± 95% Confidence Intervals	0.575 ± 0.157
Sensitivity	0.443
Positive Predictive Value	0.664
Nr of predictions	11

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
3ZEX_C	5_8S_rRNA links to Rfam database...	0.26	0.21	0.33	11	14163	35	2	20	13	41
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.59	0.97	29	6991	1	0	1	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.56	0.47	0.68	15	3464	7	1	6	0	17

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

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

Total Base Pair Counts
Total TP	137
Total TN	64080
Total FP	34
Total FP CONTRA	2
Total FP INCONS	28
Total FP COMP	4
Total FN	269

Total Scores
MCC	0.524
Average MCC ± 95% Confidence Intervals	0.445 ± 0.186
Sensitivity	0.337
Positive Predictive Value	0.820
Nr of predictions	11

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.62	0.53	0.73	16	2828	7	0	6	1	14
3J20_1	tRNA links to Rfam database...	0.86	0.74	1.00	17	2909	0	0	0	0	6
3J2L_3	5S_rRNA links to Rfam database...	0.46	0.34	0.64	18	7847	11	0	10	1	35
3ZEX_C	5_8S_rRNA links to Rfam database...	0.31	0.13	0.70	7	14186	3	1	2	0	45
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.53	1.00	26	6995	0	0	0	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.15	0.71	5	11774	3	0	2	1	28
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4AOB_A	SAM links to Rfam database...	0.49	0.33	0.74	14	4352	6	1	4	1	28
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19
4FRG_B	AdoCbl-variant links to Rfam database...	0.43	0.19	1.00	6	3480	0	0	0	0	26

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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 RNASLOpt - scored higher in this pairwise comparison

1. Total counts & total scores for RNASLOpt

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

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

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

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