CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Murlet(20)		Multilign(20)
MCC	0.664	>	0.652
Average MCC ± 95% Confidence Intervals	0.642 ± 0.128	>	0.638 ± 0.177
Sensitivity	0.573	<	0.624
Positive Predictive Value	0.779	>	0.692
Total TP	215	<	234
Total TN	24715	>	24653
Total FP	79	<	131
Total FP CONTRA	11	<	23
Total FP INCONS	50	<	81
Total FP COMP	18	<	27
Total FN	160	>	141
P-value	1.61878218056e-06

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Performance plots

Comparison of performance of Murlet(20) 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 Murlet(20) and Multilign(20)).
Comparison of performance of Murlet(20) 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 Murlet(20) 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 Murlet(20) 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 Murlet(20) and Multilign(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Murlet(20) 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 Murlet(20) and Multilign(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Murlet(20) 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 Murlet(20) and Multilign(20)).

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Performance of Murlet(20) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	215
Total TN	24715
Total FP	79
Total FP CONTRA	11
Total FP INCONS	50
Total FP COMP	18
Total FN	160

Total Scores
MCC	0.664
Average MCC ± 95% Confidence Intervals	0.642 ± 0.128
Sensitivity	0.573
Positive Predictive Value	0.779
Nr of predictions	15

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.51	0.50	0.56	9	341	8	0	7	1	9
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.44	0.20	1.00	7	2038	0	0	0	0	28
3AMU_B	tRNA links to Rfam database...	0.89	0.89	0.89	17	1138	4	0	2	2	2
3J20_0	tRNA links to Rfam database...	0.65	0.62	0.68	13	1200	6	1	5	0	8
3J20_1	tRNA links to Rfam database...	0.69	0.60	0.80	12	1097	4	0	3	1	8
3J2L_3	5S_rRNA links to Rfam database...	0.84	0.74	0.96	25	2994	4	0	1	3	9
3RKF_A	Purine links to Rfam database...	0.81	0.67	1.00	16	850	0	0	0	0	8
3SD1_A	THF links to Rfam database...	0.82	0.83	0.83	24	1504	5	4	1	0	5
3ZEX_D	5S_rRNA links to Rfam database...	0.90	0.86	0.94	30	2764	5	0	2	3	5
4A1C_3	5S_rRNA links to Rfam database...	0.72	0.59	0.88	22	2738	4	0	3	1	15
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.20	5	4491	24	5	15	4	15
4AOB_A	SAM links to Rfam database...	0.87	0.76	1.00	22	1415	3	0	0	3	7
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.57	0.33	1.00	5	491	0	0	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.19	0.17	0.25	4	1186	12	1	11	0	20

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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	234
Total TN	24653
Total FP	131
Total FP CONTRA	23
Total FP INCONS	81
Total FP COMP	27
Total FN	141

Total Scores
MCC	0.652
Average MCC ± 95% Confidence Intervals	0.638 ± 0.177
Sensitivity	0.624
Positive Predictive Value	0.692
Nr of predictions	15

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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
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2XXA_G	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	2033	12	2	10	0	35
3AMU_B	tRNA links to Rfam database...	0.71	0.74	0.70	14	1137	9	0	6	3	5
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
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	4	5	0	9
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2765	8	0	2	6	6
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	6	0	4	2	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.25	0.16	5	4485	33	9	17	7	15
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 Murlet(20) - scored higher in this pairwise comparison

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

2. Individual counts for Murlet(20) [ 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 ]