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)		MXScarna(20)
MCC	0.782	>	0.761
Average MCC ± 95% Confidence Intervals	0.772 ± 0.081	>	0.767 ± 0.073
Sensitivity	0.690	<	0.727
Positive Predictive Value	0.889	>	0.800
Total TP	506	<	533
Total TN	77570	>	77473
Total FP	148	<	288
Total FP CONTRA	21	<	56
Total FP INCONS	42	<	77
Total FP COMP	85	<	155
Total FN	227	>	200
P-value	5.19332990918e-08

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Performance plots

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

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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	506
Total TN	77570
Total FP	148
Total FP CONTRA	21
Total FP INCONS	42
Total FP COMP	85
Total FN	227

Total Scores
MCC	0.782
Average MCC ± 95% Confidence Intervals	0.772 ± 0.081
Sensitivity	0.690
Positive Predictive Value	0.889
Nr of predictions	28

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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
2KDQ_B	mir-TAR links to Rfam database...	0.62	0.40	1.00	4	170	0	0	0	0	6
2L94_A	HIV_FE links to Rfam database...	0.51	0.50	0.56	9	341	8	0	7	1	9
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	12	0	0	12	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	4	1831	3	0	0	3	7
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.44	0.20	1.00	7	2038	0	0	0	0	28
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	2	0	0	2	0
3G4S_9	5S_rRNA links to Rfam database...	0.96	0.92	1.00	24	2712	7	0	0	7	2
3GX2_A	SAM links to Rfam database...	0.92	0.86	1.00	24	1425	1	0	0	1	4
3IVN_B	Purine links to Rfam database...	0.86	0.78	0.95	18	884	1	1	0	0	5
3IZ4_A	tmRNA links to Rfam database...	0.65	0.48	0.87	46	25483	15	4	3	8	49
3IZF_C	5S_rRNA links to Rfam database...	0.90	0.89	0.91	31	2606	6	0	3	3	4
3JYV_7	tRNA links to Rfam database...	0.97	0.95	1.00	19	1092	2	0	0	2	1
3JYX_3	5S_rRNA links to Rfam database...	0.76	0.73	0.79	11	2364	20	0	3	17	4
3JYX_4	5_8S_rRNA links to Rfam database...	0.77	0.83	0.71	10	4742	15	3	1	11	2
3LA5_A	Purine links to Rfam database...	0.87	0.76	1.00	19	935	0	0	0	0	6
3NPB_A	SAM links to Rfam database...	0.75	0.57	1.00	21	2257	4	0	0	4	16
3O58_2	5S_rRNA links to Rfam database...	0.97	0.94	1.00	29	2725	7	0	0	7	2
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.36	0.50	8	4748	9	3	5	1	14
3PDR_A	ykoK links to Rfam database...	0.92	0.88	0.96	44	4794	3	1	1	1	6
3RKF_A	Purine links to Rfam database...	0.81	0.71	0.94	17	848	1	0	1	0	7
3SD1_A	THF links to Rfam database...	0.84	0.86	0.83	25	1503	5	4	1	0	4
4A1C_3	5S_rRNA links to Rfam database...	0.90	0.84	0.97	31	2731	1	0	1	0	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.19	5	4490	23	5	16	2	15
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9

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Performance of MXScarna(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	533
Total TN	77473
Total FP	288
Total FP CONTRA	56
Total FP INCONS	77
Total FP COMP	155
Total FN	200

Total Scores
MCC	0.761
Average MCC ± 95% Confidence Intervals	0.767 ± 0.073
Sensitivity	0.727
Positive Predictive Value	0.800
Nr of predictions	28

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2. Individual counts for MXScarna(20) [ 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
2L94_A	HIV_FE links to Rfam database...	0.73	0.72	0.76	13	340	5	0	4	1	5
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	4	1831	3	0	0	3	7
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.88	0.86	0.91	30	2012	4	0	3	1	5
3A2K_C	tRNA links to Rfam database...	0.74	0.73	0.76	16	1087	6	1	4	1	6
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	3	0	0	3	0
3G4S_9	5S_rRNA links to Rfam database...	0.78	0.77	0.80	20	2711	16	2	3	11	6
3GX2_A	SAM links to Rfam database...	0.81	0.79	0.85	22	1423	6	2	2	2	6
3IVN_B	Purine links to Rfam database...	0.81	0.74	0.89	17	884	2	2	0	0	6
3IZ4_A	tmRNA links to Rfam database...	0.58	0.54	0.63	51	25455	35	18	12	5	44
3IZF_C	5S_rRNA links to Rfam database...	0.87	0.89	0.86	31	2604	12	0	5	7	4
3JYV_7	tRNA links to Rfam database...	0.95	0.90	1.00	18	1093	2	0	0	2	2
3JYX_3	5S_rRNA links to Rfam database...	0.73	0.73	0.73	11	2363	26	0	4	22	4
3JYX_4	5_8S_rRNA links to Rfam database...	0.70	0.83	0.59	10	4739	32	5	2	25	2
3LA5_A	Purine links to Rfam database...	0.87	0.80	0.95	20	933	1	1	0	0	5
3NPB_A	SAM links to Rfam database...	0.77	0.73	0.82	27	2245	9	2	4	3	10
3O58_2	5S_rRNA links to Rfam database...	0.92	0.90	0.93	28	2724	13	0	2	11	3
3O58_3	5_8S_rRNA links to Rfam database...	0.62	0.59	0.65	13	4744	18	5	2	11	9
3PDR_A	ykoK links to Rfam database...	0.85	0.82	0.89	41	4794	9	2	3	4	9
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.74	0.76	0.73	22	1503	9	6	2	1	7
4A1C_3	5S_rRNA links to Rfam database...	0.80	0.78	0.83	29	2728	12	0	6	6	8
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.21	5	4492	36	8	11	17	15
4AOB_A	SAM links to Rfam database...	0.68	0.69	0.69	20	1408	13	2	7	4	9
4ENB_A	crcB links to Rfam database...	0.29	0.13	0.67	2	469	1	0	1	0	13
4ENC_A	crcB links to Rfam database...	0.68	0.47	1.00	7	489	0	0	0	0	8

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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 MXScarna(20) - scored lower in this pairwise comparison

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

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