CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MCFold		Carnac(seed)
MCC	0.639	>	0.314
Average MCC ± 95% Confidence Intervals	0.659 ± 0.118	>	0.181 ± 0.129
Sensitivity	0.684	>	0.100
Positive Predictive Value	0.606	<	1.000
Total TP	439	>	64
Total TN	45643	<	46303
Total FP	372	>	1
Total FP CONTRA	85	>	0
Total FP INCONS	200	>	0
Total FP COMP	87	>	1
Total FN	203	<	578
P-value	5.19332990918e-08

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Performance plots

Comparison of performance of MCFold and Carnac(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 MCFold and Carnac(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 MCFold and Carnac(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for MCFold and Carnac(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 MCFold and Carnac(seed)).

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Performance of MCFold - scored higher in this pairwise comparison

1. Total counts & total scores for MCFold

Total Base Pair Counts
Total TP	439
Total TN	45643
Total FP	372
Total FP CONTRA	85
Total FP INCONS	200
Total FP COMP	87
Total FN	203

Total Scores
MCC	0.639
Average MCC ± 95% Confidence Intervals	0.659 ± 0.118
Sensitivity	0.684
Positive Predictive Value	0.606
Nr of predictions	28

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2. Individual counts for MCFold [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	1	0	0	1	0
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	449	1	0	0	1	0
2KUR_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	448	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	429	1	0	0	1	0
2KUV_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	420	0	0	0	0	0
2KUW_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	452	1	0	0	1	0
2L1F_A	Gammaretro_CES links to Rfam database...	0.79	0.78	0.82	18	741	4	0	4	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.80	0.79	0.83	19	768	4	0	4	0	5
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.44	0.44	0.47	8	511	10	0	9	1	10
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.20	0.27	0.16	3	1816	30	4	12	14	8
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.23	0.26	0.24	9	2007	30	1	28	1	26
3A3A_A	tRNA-Sec links to Rfam database...	0.98	0.97	1.00	29	1471	0	0	0	0	1
3GX2_A	SAM links to Rfam database...	0.58	0.61	0.57	17	1419	15	1	12	2	11
3IVN_B	Purine links to Rfam database...	0.45	0.48	0.46	11	879	14	5	8	1	12
3IZF_C	5S_rRNA links to Rfam database...	0.92	0.94	0.89	33	2603	10	0	4	6	2
3JYX_4	5_8S_rRNA links to Rfam database...	0.36	0.58	0.23	7	4725	37	19	5	13	5
3JYX_3	5S_rRNA links to Rfam database...	0.46	0.67	0.32	10	2347	28	15	6	7	5
3LA5_A	Purine links to Rfam database...	0.44	0.44	0.48	11	931	12	2	10	0	14
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.36	0.22	8	4727	39	14	15	10	14
3O58_2	5S_rRNA links to Rfam database...	0.25	0.29	0.23	9	2715	31	6	24	1	22
3PDR_A	ykoK links to Rfam database...	0.78	0.80	0.77	40	4788	14	5	7	2	10
3RKF_A	Purine links to Rfam database...	0.89	0.88	0.91	21	843	3	0	2	1	3
3SD1_A	THF links to Rfam database...	0.43	0.45	0.43	13	1503	17	1	16	0	16
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	45	12	19	14	15
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.86	0.86	32	2726	9	0	5	4	5
4ENB_A	crcB links to Rfam database...	0.78	0.73	0.85	11	459	4	0	2	2	4
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	11	0	8	3	10

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

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

Total Base Pair Counts
Total TP	64
Total TN	46303
Total FP	1
Total FP CONTRA	0
Total FP INCONS	0
Total FP COMP	1
Total FN	578

Total Scores
MCC	0.314
Average MCC ± 95% Confidence Intervals	0.181 ± 0.129
Sensitivity	0.100
Positive Predictive Value	1.000
Nr of predictions	28

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	0.00	0.00	0.00	0	467	0	0	0	0	18
2KUR_A	K10_TLS links to Rfam database...	0.60	0.37	1.00	7	460	0	0	0	0	12
2KUU_A	K10_TLS links to Rfam database...	0.62	0.39	1.00	7	440	0	0	0	0	11
2KUV_A	K10_TLS links to Rfam database...	0.68	0.47	1.00	9	430	0	0	0	0	10
2KUW_A	K10_TLS links to Rfam database...	0.70	0.50	1.00	9	461	0	0	0	0	9
2L1F_A	Gammaretro_CES links to Rfam database...	0.00	0.00	0.00	0	763	0	0	0	0	23
2L1F_B	Gammaretro_CES links to Rfam database...	0.00	0.00	0.00	0	791	0	0	0	0	24
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.47	0.22	1.00	4	524	0	0	0	0	14
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	1835	0	0	0	0	11
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	2045	0	0	0	0	35
3A3A_A	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	1500	0	0	0	0	30
3GX2_A	SAM links to Rfam database...	0.00	0.00	0.00	0	1449	0	0	0	0	28
3IVN_B	Purine links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	23
3IZF_C	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2640	0	0	0	0	35
3JYX_4	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4756	0	0	0	0	12
3JYX_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2378	0	0	0	0	15
3LA5_A	Purine links to Rfam database...	0.00	0.00	0.00	0	954	0	0	0	0	25
3O58_3	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4764	0	0	0	0	22
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2754	0	0	0	0	31
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	4840	0	0	0	0	50
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
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...	0.00	0.00	0.00	0	2763	0	0	0	0	37
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

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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 MCFold - scored higher in this pairwise comparison

1. Total counts & total scores for MCFold

2. Individual counts for MCFold [ download as .csv ]

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

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

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