CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ProbKnot		PPfold(seed)
MCC	0.641	>	0.094
Average MCC ± 95% Confidence Intervals	0.625 ± 0.130	>	0.039 ± 0.056
Sensitivity	0.655	>	0.019
Positive Predictive Value	0.638	>	0.474
Total TP	306	>	9
Total TN	34300	<	34761
Total FP	225	>	49
Total FP CONTRA	54	>	0
Total FP INCONS	120	>	10
Total FP COMP	51	>	39
Total FN	161	<	458
P-value	1.79203144115e-08

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Performance plots

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

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Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	306
Total TN	34300
Total FP	225
Total FP CONTRA	54
Total FP INCONS	120
Total FP COMP	51
Total FN	161

Total Scores
MCC	0.641
Average MCC ± 95% Confidence Intervals	0.625 ± 0.130
Sensitivity	0.655
Positive Predictive Value	0.638
Nr of predictions	19

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2. Individual counts for ProbKnot [ 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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	9	0	5	4	4
3J16_L	tRNA links to Rfam database...	0.42	0.48	0.38	10	1133	16	3	13	0	11
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	8	0	5	3	5
3J2L_3	5S_rRNA links to Rfam database...	0.79	0.76	0.81	26	2988	11	0	6	5	8
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.66	0.69	0.65	20	1502	11	6	5	0	9
3UZL_B	tRNA links to Rfam database...	0.92	1.00	0.84	16	1274	11	3	0	8	0
3W3S_B	tRNA-Sec links to Rfam database...	0.98	0.97	1.00	32	1957	1	0	0	1	1
3ZEX_C	5_8S_rRNA links to Rfam database...	0.48	0.52	0.45	15	5341	22	4	14	4	14
3ZEX_D	5S_rRNA links to Rfam database...	0.90	0.86	0.94	30	2764	7	0	2	5	5
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	7	0	4	3	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.25	0.13	5	4477	49	13	21	15	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...	0.81	0.73	0.92	11	460	1	1	0	0	4
4ENC_A	crcB links to Rfam database...	0.52	0.53	0.53	8	481	8	0	7	1	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.38	0.38	0.41	9	1180	13	6	7	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.49	0.46	0.54	13	1824	11	6	5	0	15

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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 ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

2. Individual counts for ProbKnot [ 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 ]