CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAalifold(20)		MaxExpect
MCC	0.655	>	0.580
Average MCC ± 95% Confidence Intervals	0.653 ± 0.066	>	0.583 ± 0.073
Sensitivity	0.504	>	0.503
Positive Predictive Value	0.855	>	0.674
Total TP	623	>	622
Total TN	239944	>	239750
Total FP	147	<	393
Total FP CONTRA	21	<	34
Total FP INCONS	85	<	267
Total FP COMP	41	<	92
Total FN	614	<	615
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RNAalifold(20) and MaxExpect. 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 RNAalifold(20) and MaxExpect).
Comparison of performance of RNAalifold(20) and MaxExpect. 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 RNAalifold(20) and MaxExpect).
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 RNAalifold(20) and MaxExpect).
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 RNAalifold(20) and MaxExpect).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(20) and MaxExpect. 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 RNAalifold(20) and MaxExpect).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(20) and MaxExpect. 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 RNAalifold(20) and MaxExpect).

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Performance of RNAalifold(20) - scored higher in this pairwise comparison

1. Total counts & total scores for RNAalifold(20)

Total Base Pair Counts
Total TP	623
Total TN	239944
Total FP	147
Total FP CONTRA	21
Total FP INCONS	85
Total FP COMP	41
Total FN	614

Total Scores
MCC	0.655
Average MCC ± 95% Confidence Intervals	0.653 ± 0.066
Sensitivity	0.504
Positive Predictive Value	0.855
Nr of predictions	32

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2. Individual counts for RNAalifold(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.53	0.50	0.59	10	973	7	0	7	0	10
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	11	5	3	3	7
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	4	4556	3	0	0	3	16
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.41	0.17	1.00	7	5144	0	0	0	0	35
3A2K_C	tRNA links to Rfam database...	0.86	0.75	1.00	21	2905	0	0	0	0	7
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	1	0	0	1	7
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...	0.74	0.58	0.95	18	2327	1	1	0	0	13
3IZ4_A	tmRNA links to Rfam database...	0.53	0.35	0.82	46	70820	15	4	6	5	86
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.59	0.86	32	6866	5	1	4	0	22
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	0	0	0	0	9
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2L_3	5S_rRNA links to Rfam database...	0.69	0.47	1.00	25	7850	2	0	0	2	28
3JYV_7	tRNA links to Rfam database...	0.81	0.66	1.00	21	2829	0	0	0	0	11
3JYX_3	5S_rRNA links to Rfam database...	0.60	0.52	0.70	14	6308	17	0	6	11	13
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.30	0.50	10	12226	15	0	10	5	23
3LA5_A	Purine links to Rfam database...	0.75	0.56	1.00	19	2466	0	0	0	0	15
3NPB_A	SAM links to Rfam database...	0.68	0.48	0.96	22	6998	3	1	0	2	24
3O58_3	5_8S_rRNA links to Rfam database...	0.37	0.26	0.53	9	12386	8	2	6	0	26
3O58_2	5S_rRNA links to Rfam database...	0.79	0.76	0.83	29	7225	7	3	3	1	9
3PDR_A	ykoK links to Rfam database...	0.76	0.61	0.96	44	12834	3	0	2	1	28
3RKF_A	Purine links to Rfam database...	0.68	0.50	0.94	17	2193	1	0	1	0	17
3SD1_A	THF links to Rfam database...	0.70	0.60	0.83	25	3886	5	1	4	0	17
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.27	0.56	14	14171	14	1	10	3	38
3ZEX_D	5S_rRNA links to Rfam database...	0.80	0.69	0.92	34	6984	3	0	3	0	15
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	23	2	19	2	28
4A1C_3	5S_rRNA links to Rfam database...	0.74	0.57	0.97	31	7108	1	0	1	0	23
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENB_A	crcB links to Rfam database...	0.46	0.21	1.00	4	1271	0	0	0	0	15
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...	0.73	0.53	1.00	17	3469	0	0	0	0	15

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Performance of MaxExpect - scored lower in this pairwise comparison

1. Total counts & total scores for MaxExpect

Total Base Pair Counts
Total TP	622
Total TN	239750
Total FP	393
Total FP CONTRA	34
Total FP INCONS	267
Total FP COMP	92
Total FN	615

Total Scores
MCC	0.580
Average MCC ± 95% Confidence Intervals	0.583 ± 0.073
Sensitivity	0.503
Positive Predictive Value	0.674
Nr of predictions	32

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2WRQ_Y	tRNA links to Rfam database...	0.53	0.53	0.53	9	2833	13	5	3	5	8
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	24	0	9	15	10
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.25	0.24	0.27	10	5114	27	1	26	0	32
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3GX2_A	SAM links to Rfam database...	0.77	0.63	0.96	25	4345	2	0	1	1	15
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IZ4_A	tmRNA links to Rfam database...	0.54	0.46	0.64	61	70781	39	3	31	5	71
3IZF_C	5S_rRNA links to Rfam database...	0.71	0.61	0.83	33	6863	7	1	6	0	21
3J20_0	tRNA links to Rfam database...	0.44	0.40	0.50	12	2826	13	0	12	1	18
3J20_1	tRNA links to Rfam database...	0.73	0.70	0.76	16	2905	5	0	5	0	7
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
3JYV_7	tRNA links to Rfam database...	0.41	0.31	0.56	10	2832	8	0	8	0	22
3JYX_3	5S_rRNA links to Rfam database...	0.64	0.63	0.65	17	6302	19	1	8	10	10
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.31	10	12214	34	4	18	12	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	0.61	0.82	28	6987	9	0	6	3	18
3O58_3	5_8S_rRNA links to Rfam database...	0.35	0.34	0.35	12	12369	35	2	20	13	23
3O58_2	5S_rRNA links to Rfam database...	0.75	0.76	0.74	29	7221	11	3	7	1	9
3PDR_A	ykoK links to Rfam database...	0.76	0.63	0.94	45	12832	5	0	3	2	27
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...	0.58	0.48	0.71	20	3888	8	1	7	0	22
3ZEX_C	5_8S_rRNA links to Rfam database...	0.41	0.27	0.64	14	14174	16	2	6	8	38
3ZEX_D	5S_rRNA links to Rfam database...	0.69	0.61	0.79	30	6983	8	1	7	0	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11746	41	4	26	11	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.31	0.26	0.38	5	1313	8	1	7	0	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.30	0.22	0.41	7	3469	10	1	9	0	25

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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 RNAalifold(20) - scored higher in this pairwise comparison

1. Total counts & total scores for RNAalifold(20)

2. Individual counts for RNAalifold(20) [ download as .csv ]

Performance of MaxExpect - scored lower in this pairwise comparison

1. Total counts & total scores for MaxExpect

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