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		Mastr(20)
MCC	0.635	>	0.561
Average MCC ± 95% Confidence Intervals	0.657 ± 0.163	>	0.442 ± 0.244
Sensitivity	0.616	>	0.430
Positive Predictive Value	0.662	<	0.741
Total TP	172	>	120
Total TN	24147	<	24245
Total FP	121	>	54
Total FP CONTRA	31	>	5
Total FP INCONS	57	>	37
Total FP COMP	33	>	12
Total FN	107	<	159
P-value	1.74172190343e-08

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Performance plots

Comparison of performance of RNASLOpt and Mastr(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 Mastr(20)).
Comparison of performance of RNASLOpt and Mastr(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 Mastr(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 Mastr(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 Mastr(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASLOpt and Mastr(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 Mastr(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASLOpt and Mastr(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 Mastr(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	172
Total TN	24147
Total FP	121
Total FP CONTRA	31
Total FP INCONS	57
Total FP COMP	33
Total FN	107

Total Scores
MCC	0.635
Average MCC ± 95% Confidence Intervals	0.657 ± 0.163
Sensitivity	0.616
Positive Predictive Value	0.662
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...	0.74	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_C	5_8S_rRNA links to Rfam database...	0.32	0.34	0.31	10	5342	36	8	14	14	19
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 Mastr(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	120
Total TN	24245
Total FP	54
Total FP CONTRA	5
Total FP INCONS	37
Total FP COMP	12
Total FN	159

Total Scores
MCC	0.561
Average MCC ± 95% Confidence Intervals	0.442 ± 0.244
Sensitivity	0.430
Positive Predictive Value	0.741
Nr of predictions	11

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2. Individual counts for Mastr(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...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J20_1	tRNA links to Rfam database...	0.26	0.25	0.29	5	1095	12	1	11	0	15
3J2L_3	5S_rRNA links to Rfam database...	0.42	0.38	0.48	13	2993	16	2	12	2	21
3ZEX_C	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	5374	0	0	0	0	29
3ZEX_D	5S_rRNA links to Rfam database...	0.93	0.91	0.94	32	2762	7	0	2	5	3
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4516	0	0	0	0	20
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	7	0	4	3	5
4AOB_A	SAM links to Rfam database...	0.42	0.34	0.53	10	1418	10	1	8	1	19
4ENB_A	crcB links to Rfam database...	0.44	0.20	1.00	3	469	0	0	0	0	12
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...	0.00	0.00	0.00	0	1202	0	0	0	0	24

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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 Mastr(20) - scored lower in this pairwise comparison

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

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