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		Multilign(20)
MCC	0.674	>	0.657
Average MCC ± 95% Confidence Intervals	0.690 ± 0.163	>	0.627 ± 0.213
Sensitivity	0.648	>	0.644
Positive Predictive Value	0.711	>	0.679
Total TP	162	>	161
Total TN	18805	>	18796
Total FP	85	<	99
Total FP CONTRA	23	>	17
Total FP INCONS	43	<	59
Total FP COMP	19	<	23
Total FN	88	<	89
P-value	1.1688086697e-05

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Performance plots

Comparison of performance of RNASLOpt and Multilign(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 Multilign(20)).
Comparison of performance of RNASLOpt and Multilign(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 Multilign(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 Multilign(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 Multilign(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASLOpt and Multilign(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 Multilign(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASLOpt and Multilign(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 Multilign(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	162
Total TN	18805
Total FP	85
Total FP CONTRA	23
Total FP INCONS	43
Total FP COMP	19
Total FN	88

Total Scores
MCC	0.674
Average MCC ± 95% Confidence Intervals	0.690 ± 0.163
Sensitivity	0.648
Positive Predictive Value	0.711
Nr of predictions	10

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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...	0.74	0.76	0.73	16	1197	7	3	3	1	5
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...	0.71	0.68	0.74	23	2989	11	0	8	3	11
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.74	1.00	26	2770	4	0	0	4	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.30	0.40	0.24	8	4482	35	13	13	9	12
4A1C_3	5S_rRNA links to Rfam database...	0.79	0.73	0.87	27	2732	5	0	4	1	10
4AOB_A	SAM links to Rfam database...	0.31	0.28	0.38	8	1416	13	3	10	0	21
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10

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

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

Total Base Pair Counts
Total TP	161
Total TN	18796
Total FP	99
Total FP CONTRA	17
Total FP INCONS	59
Total FP COMP	23
Total FN	89

Total Scores
MCC	0.657
Average MCC ± 95% Confidence Intervals	0.627 ± 0.213
Sensitivity	0.644
Positive Predictive Value	0.679
Nr of predictions	10

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2. Individual counts for Multilign(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...	0.68	0.71	0.65	15	1196	9	2	6	1	6
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...	0.80	0.79	0.82	27	2987	10	0	6	4	7
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2765	8	0	2	6	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.25	0.16	5	4485	33	9	17	7	15
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	6	0	4	2	5
4AOB_A	SAM links to Rfam database...	0.59	0.55	0.64	16	1412	10	3	6	1	13
4ENB_A	crcB links to Rfam database...	0.39	0.33	0.50	5	462	6	0	5	1	10
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.13	0.13	0.17	3	1184	15	2	13	0	21

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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 Multilign(20) - scored lower in this pairwise comparison

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

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