CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CentroidAlifold(seed)		Murlet(seed)
MCC	0.677	>	0.447
Average MCC ± 95% Confidence Intervals	0.637 ± 0.085	>	0.441 ± 0.067
Sensitivity	0.481	>	0.244
Positive Predictive Value	0.955	>	0.823
Total TP	402	>	204
Total TN	137777	<	137950
Total FP	30	<	51
Total FP CONTRA	6	=	6
Total FP INCONS	13	<	38
Total FP COMP	11	>	7
Total FN	433	<	631
P-value	5.10776592382e-08

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Performance plots

Comparison of performance of CentroidAlifold(seed) and Murlet(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 CentroidAlifold(seed) and Murlet(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 CentroidAlifold(seed) and Murlet(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(seed) and Murlet(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 CentroidAlifold(seed) and Murlet(seed)).

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Performance of CentroidAlifold(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidAlifold(seed)

Total Base Pair Counts
Total TP	402
Total TN	137777
Total FP	30
Total FP CONTRA	6
Total FP INCONS	13
Total FP COMP	11
Total FN	433

Total Scores
MCC	0.677
Average MCC ± 95% Confidence Intervals	0.637 ± 0.085
Sensitivity	0.481
Positive Predictive Value	0.955
Nr of predictions	23

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2. Individual counts for CentroidAlifold(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...	0.00	0.00	0.00	0	1540	0	0	0	0	20
3A3A_A	tRNA-Sec links to Rfam database...	0.85	0.73	1.00	27	3628	0	0	0	0	10
3GX2_A	SAM links to Rfam database...	0.77	0.60	1.00	24	4347	1	0	0	1	16
3IVN_B	Purine links to Rfam database...	0.78	0.65	0.95	20	2325	1	1	0	0	11
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.09	0.75	3	7499	1	0	1	0	30
3J3F_8	5_8S_rRNA links to Rfam database...	0.55	0.33	0.92	12	12233	1	0	1	0	24
3JYX_4	5_8S_rRNA links to Rfam database...	0.52	0.30	0.91	10	12235	3	0	1	2	23
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.71	0.54	0.93	25	6994	4	1	1	2	21
3O58_3	5_8S_rRNA links to Rfam database...	0.56	0.34	0.92	12	12390	1	0	1	0	23
3PDR_A	ykoK links to Rfam database...	0.77	0.61	0.98	44	12835	3	0	1	2	28
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.71	0.52	0.96	22	3893	1	0	1	0	20
3W1K_J	tRNA-Sec links to Rfam database...	0.78	0.66	0.93	25	4159	2	1	1	0	13
3W3S_B	tRNA-Sec links to Rfam database...	0.74	0.60	0.92	24	4727	3	0	2	1	16
3ZEX_C	5_8S_rRNA links to Rfam database...	0.46	0.23	0.92	12	14183	1	1	0	0	40
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.24	0.89	8	11772	3	0	1	2	25
4AOB_A	SAM links to Rfam database...	0.75	0.57	1.00	24	4347	1	0	0	1	18
4ENB_A	crcB links to Rfam database...	0.65	0.42	1.00	8	1267	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.65	0.42	1.00	8	1318	0	0	0	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.69	0.53	0.89	17	3467	2	1	1	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.71	0.56	0.91	20	5129	2	1	1	0	16
4JF2_A	preQ1-II links to Rfam database...	0.72	0.52	1.00	16	2834	0	0	0	0	15

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Performance of Murlet(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	204
Total TN	137950
Total FP	51
Total FP CONTRA	6
Total FP INCONS	38
Total FP COMP	7
Total FN	631

Total Scores
MCC	0.447
Average MCC ± 95% Confidence Intervals	0.441 ± 0.067
Sensitivity	0.244
Positive Predictive Value	0.823
Nr of predictions	23

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2. Individual counts for Murlet(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...	-0.01	0.00	0.00	0	1528	12	0	12	0	20
3A3A_A	tRNA-Sec links to Rfam database...	0.57	0.32	1.00	12	3643	0	0	0	0	25
3GX2_A	SAM links to Rfam database...	0.59	0.35	1.00	14	4357	1	0	0	1	26
3IVN_B	Purine links to Rfam database...	0.53	0.39	0.75	12	2330	4	2	2	0	19
3J3E_8	5_8S_rRNA links to Rfam database...	0.25	0.06	1.00	2	7501	2	0	0	2	31
3J3F_8	5_8S_rRNA links to Rfam database...	0.44	0.19	1.00	7	12239	0	0	0	0	29
3JYX_4	5_8S_rRNA links to Rfam database...	0.23	0.09	0.60	3	12241	4	0	2	2	30
3LA5_A	Purine links to Rfam database...	0.58	0.41	0.82	14	2468	3	1	2	0	20
3NPB_A	SAM links to Rfam database...	0.49	0.28	0.87	13	7006	2	1	1	0	33
3O58_3	5_8S_rRNA links to Rfam database...	0.45	0.20	1.00	7	12396	0	0	0	0	28
3PDR_A	ykoK links to Rfam database...	0.44	0.19	1.00	14	12866	0	0	0	0	58
3RKF_A	Purine links to Rfam database...	0.53	0.35	0.80	12	2196	3	1	2	0	22
3SD1_A	THF links to Rfam database...	0.47	0.26	0.85	11	3903	2	0	2	0	31
3W1K_J	tRNA-Sec links to Rfam database...	0.43	0.21	0.89	8	4177	1	0	1	0	30
3W3S_B	tRNA-Sec links to Rfam database...	0.41	0.23	0.75	9	4741	3	0	3	0	31
3ZEX_C	5_8S_rRNA links to Rfam database...	0.37	0.13	1.00	7	14189	0	0	0	0	45
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	11774	0	0	0	0	26
4AOB_A	SAM links to Rfam database...	0.58	0.33	1.00	14	4357	1	0	0	1	28
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13
4FRG_B	AdoCbl-variant links to Rfam database...	0.15	0.09	0.25	3	3474	9	0	9	0	29
4FRN_A	AdoCbl-variant links to Rfam database...	0.58	0.39	0.88	14	5135	2	1	1	0	22
4JF2_A	preQ1-II links to Rfam database...	0.51	0.29	0.90	9	2840	2	0	1	1	22

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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 CentroidAlifold(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidAlifold(seed)

2. Individual counts for CentroidAlifold(seed) [ download as .csv ]

Performance of Murlet(seed) - scored lower in this pairwise comparison

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

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