CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Pknots		Carnac(seed)
MCC	0.708	>	0.299
Average MCC ± 95% Confidence Intervals	0.749 ± 0.111	>	0.169 ± 0.121
Sensitivity	0.744	>	0.090
Positive Predictive Value	0.682	<	1.000
Total TP	527	>	64
Total TN	49309	<	50018
Total FP	326	>	1
Total FP CONTRA	89	>	0
Total FP INCONS	157	>	0
Total FP COMP	80	>	1
Total FN	181	<	644
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Pknots - scored higher in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	527
Total TN	49309
Total FP	326
Total FP CONTRA	89
Total FP INCONS	157
Total FP COMP	80
Total FN	181

Total Scores
MCC	0.708
Average MCC ± 95% Confidence Intervals	0.749 ± 0.111
Sensitivity	0.744
Positive Predictive Value	0.682
Nr of predictions	30

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2. Individual counts for Pknots [ 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...	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...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	0.94	0.94	0.94	17	339	2	0	1	1	1
2LC8_A	GP_knot1 links to Rfam database...	0.83	0.83	0.83	15	510	3	2	1	0	3
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.21	0.27	0.17	3	1817	33	3	12	18	8
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.32	0.34	0.32	12	2008	26	1	24	1	23
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.55	0.57	0.55	16	1420	14	4	9	1	12
3IVN_B	Purine links to Rfam database...	0.91	0.87	0.95	20	882	1	0	1	0	3
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	9	0	5	4	3
3JYX_4	5_8S_rRNA links to Rfam database...	0.33	0.58	0.19	7	4720	41	22	7	12	5
3JYX_3	5S_rRNA links to Rfam database...	0.37	0.53	0.27	8	2348	26	17	5	4	7
3LA5_A	Purine links to Rfam database...	0.94	0.88	1.00	22	932	0	0	0	0	3
3NPB_A	SAM links to Rfam database...	0.84	0.81	0.88	30	2244	9	0	4	5	7
3O58_2	5S_rRNA links to Rfam database...	0.93	0.90	0.97	28	2725	3	0	1	2	3
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.45	0.24	10	4722	39	18	14	7	12
3PDR_A	ykoK links to Rfam database...	0.64	0.64	0.65	32	4791	19	4	13	2	18
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...	0.78	0.76	0.81	22	1506	5	1	4	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.29	8	4488	36	9	11	16	12
4A1C_3	5S_rRNA links to Rfam database...	0.28	0.30	0.28	11	2723	30	4	25	1	26
4AOB_A	SAM links to Rfam database...	0.19	0.21	0.21	6	1409	23	3	19	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	2	0	0	2	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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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	50018
Total FP	1
Total FP CONTRA	0
Total FP INCONS	0
Total FP COMP	1
Total FN	644

Total Scores
MCC	0.299
Average MCC ± 95% Confidence Intervals	0.169 ± 0.121
Sensitivity	0.090
Positive Predictive Value	1.000
Nr of predictions	30

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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
3NPB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	2278	0	0	0	0	37
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2754	0	0	0	0	31
3O58_3	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4764	0	0	0	0	22
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
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

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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 Pknots - scored higher in this pairwise comparison

1. Total counts & total scores for Pknots

2. Individual counts for Pknots [ 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 ]