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)		MCFold
MCC	0.603	>	0.442
Average MCC ± 95% Confidence Intervals	0.537 ± 0.084	>	0.438 ± 0.086
Sensitivity	0.377	<	0.466
Positive Predictive Value	0.971	>	0.427
Total TP	333	<	412
Total TN	125950	>	125329
Total FP	22	<	602
Total FP CONTRA	1	<	82
Total FP INCONS	9	<	470
Total FP COMP	12	<	50
Total FN	551	>	472
P-value	5.19332990918e-08

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Performance plots

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

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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	333
Total TN	125950
Total FP	22
Total FP CONTRA	1
Total FP INCONS	9
Total FP COMP	12
Total FN	551

Total Scores
MCC	0.603
Average MCC ± 95% Confidence Intervals	0.537 ± 0.084
Sensitivity	0.377
Positive Predictive Value	0.971
Nr of predictions	27

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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
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	861	0	0	0	0	18
2LC8_A	GP_knot1 links to Rfam database...	0.00	0.00	0.00	0	1540	0	0	0	0	20
2WRQ_Y	tRNA links to Rfam database...	0.24	0.12	0.50	2	2846	4	0	2	2	15
2WWQ_V	tRNA links to Rfam database...	0.46	0.21	1.00	6	2920	0	0	0	0	22
2XQD_Y	tRNA links to Rfam database...	0.47	0.22	1.00	6	2844	0	0	0	0	21
2ZZN_D	tRNA links to Rfam database...	0.47	0.22	1.00	6	2479	0	0	0	0	21
3A2K_C	tRNA links to Rfam database...	0.46	0.21	1.00	6	2920	0	0	0	0	22
3A3A_A	tRNA-Sec links to Rfam database...	0.85	0.73	1.00	27	3628	0	0	0	0	10
3AKZ_H	tRNA links to Rfam database...	0.46	0.21	1.00	6	2695	0	0	0	0	22
3AMU_B	tRNA links to Rfam database...	0.47	0.22	1.00	6	2997	0	0	0	0	21
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
3IZF_C	5S_rRNA links to Rfam database...	0.54	0.30	1.00	16	6887	0	0	0	0	38
3J16_L	tRNA links to Rfam database...	0.45	0.20	1.00	6	2769	0	0	0	0	24
3JYV_7	tRNA links to Rfam database...	0.43	0.19	1.00	6	2844	0	0	0	0	26
3JYX_4	5_8S_rRNA links to Rfam database...	0.52	0.30	0.91	10	12235	3	0	1	2	23
3JYX_3	5S_rRNA links to Rfam database...	0.59	0.41	0.85	11	6315	5	0	2	3	16
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3O58_2	5S_rRNA links to Rfam database...	0.65	0.42	1.00	16	7244	0	0	0	0	22
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.24	0.89	8	11772	3	0	1	2	25
4A1C_3	5S_rRNA links to Rfam database...	0.54	0.30	1.00	16	7124	0	0	0	0	38
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

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Performance of MCFold - scored lower in this pairwise comparison

1. Total counts & total scores for MCFold

Total Base Pair Counts
Total TP	412
Total TN	125329
Total FP	602
Total FP CONTRA	82
Total FP INCONS	470
Total FP COMP	50
Total FN	472

Total Scores
MCC	0.442
Average MCC ± 95% Confidence Intervals	0.438 ± 0.086
Sensitivity	0.466
Positive Predictive Value	0.427
Nr of predictions	27

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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
2KX8_A	7SK links to Rfam database...	0.91	0.89	0.94	16	844	2	0	1	1	2
2LC8_A	GP_knot1 links to Rfam database...	0.41	0.45	0.39	9	1517	16	0	14	2	11
2WRQ_Y	tRNA links to Rfam database...	0.27	0.35	0.22	6	2823	25	8	13	4	11
2WWQ_V	tRNA links to Rfam database...	0.15	0.18	0.15	5	2892	30	4	25	1	23
2XQD_Y	tRNA links to Rfam database...	0.34	0.37	0.32	10	2819	22	1	20	1	17
2ZZN_D	tRNA links to Rfam database...	0.61	0.63	0.61	17	2457	13	1	10	2	10
3A2K_C	tRNA links to Rfam database...	0.44	0.46	0.42	13	2895	18	2	16	0	15
3A3A_A	tRNA-Sec links to Rfam database...	0.89	0.86	0.91	32	3620	3	1	2	0	5
3AKZ_H	tRNA links to Rfam database...	0.40	0.43	0.39	12	2670	19	3	16	0	16
3AMU_B	tRNA links to Rfam database...	0.44	0.48	0.42	13	2972	18	2	16	0	14
3GX2_A	SAM links to Rfam database...	0.47	0.48	0.48	19	4331	22	0	21	1	21
3IVN_B	Purine links to Rfam database...	0.39	0.39	0.40	12	2316	18	0	18	0	19
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.69	0.74	37	6853	14	0	13	1	17
3J16_L	tRNA links to Rfam database...	0.45	0.47	0.44	14	2743	19	1	17	1	16
3JYV_7	tRNA links to Rfam database...	0.21	0.22	0.21	7	2817	26	0	26	0	25
3JYX_4	5_8S_rRNA links to Rfam database...	0.20	0.24	0.17	8	12199	43	16	23	4	25
3JYX_3	5S_rRNA links to Rfam database...	0.41	0.52	0.33	14	6285	34	12	17	5	13
3LA5_A	Purine links to Rfam database...	0.32	0.32	0.34	11	2453	21	1	20	0	23
3O58_2	5S_rRNA links to Rfam database...	0.20	0.24	0.17	9	7208	44	5	38	1	29
3O58_3	5_8S_rRNA links to Rfam database...	0.22	0.26	0.19	9	12355	45	9	30	6	26
3PDR_A	ykoK links to Rfam database...	0.66	0.61	0.72	44	12819	19	0	17	2	28
3RKF_A	Purine links to Rfam database...	0.70	0.65	0.76	22	2182	7	1	6	0	12
3SD1_A	THF links to Rfam database...	0.33	0.33	0.35	14	3876	26	0	26	0	28
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.11	5	11735	56	10	31	15	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.67	0.71	36	7089	17	1	14	2	18
4ENB_A	crcB links to Rfam database...	0.61	0.63	0.60	12	1255	8	2	6	0	7
4ENC_A	crcB links to Rfam database...	0.28	0.32	0.27	6	1304	17	2	14	1	13

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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 MCFold - scored lower in this pairwise comparison

1. Total counts & total scores for MCFold

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