CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	PETfold_pre2.0(seed)		RNASLOpt
MCC	0.867	>	0.591
Average MCC ± 95% Confidence Intervals	0.836 ± 0.062	>	0.590 ± 0.115
Sensitivity	0.826	>	0.579
Positive Predictive Value	0.913	>	0.613
Total TP	502	>	352
Total TN	51427	>	51403
Total FP	151	<	305
Total FP CONTRA	17	<	71
Total FP INCONS	31	<	151
Total FP COMP	103	>	83
Total FN	106	<	256
P-value	5.1503931209e-08

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Performance plots

Comparison of performance of PETfold_pre2.0(seed) and RNASLOpt. 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 PETfold_pre2.0(seed) and RNASLOpt).
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 PETfold_pre2.0(seed) and RNASLOpt).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and RNASLOpt. 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 PETfold_pre2.0(seed) and RNASLOpt).

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Performance of PETfold_pre2.0(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(seed)

Total Base Pair Counts
Total TP	502
Total TN	51427
Total FP	151
Total FP CONTRA	17
Total FP INCONS	31
Total FP COMP	103
Total FN	106

Total Scores
MCC	0.867
Average MCC ± 95% Confidence Intervals	0.836 ± 0.062
Sensitivity	0.826
Positive Predictive Value	0.913
Nr of predictions	25

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2. Individual counts for PETfold_pre2.0(seed) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.41	0.33	0.55	6	517	5	0	5	0	12
3J16_L	tRNA links to Rfam database...	1.00	1.00	1.00	21	1138	1	0	0	1	0
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	2	0	0	2	0
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J2L_3	5S_rRNA links to Rfam database...	0.97	0.94	1.00	32	2988	5	0	0	5	2
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	4	3	0	1	1
3J3E_8	5_8S_rRNA links to Rfam database...	0.71	0.67	0.77	10	2729	8	1	2	5	5
3J3E_7	5S_rRNA links to Rfam database...	0.97	0.97	0.97	33	2707	6	0	1	5	1
3J3F_7	5S_rRNA links to Rfam database...	0.99	0.97	1.00	35	2899	4	0	0	4	1
3J3F_8	5_8S_rRNA links to Rfam database...	0.86	0.84	0.89	16	4743	13	2	0	11	3
3J3V_B	5S_rRNA links to Rfam database...	0.90	0.89	0.92	24	2630	14	0	2	12	3
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	8	0	0	8	2
3W1K_J	tRNA-Sec links to Rfam database...	0.85	0.81	0.89	25	1650	4	2	1	1	6
3W3S_B	tRNA-Sec links to Rfam database...	0.80	0.73	0.89	24	1962	6	1	2	3	9
3ZEX_D	5S_rRNA links to Rfam database...	0.96	0.94	0.97	33	2762	6	0	1	5	2
3ZEX_C	5_8S_rRNA links to Rfam database...	0.70	0.59	0.85	17	5354	12	1	2	9	12
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	16	0	4	12	2
4A1C_2	5_8S_rRNA links to Rfam database...	0.79	0.75	0.83	15	4498	12	1	2	9	5
4A1C_3	5S_rRNA links to Rfam database...	1.00	1.00	1.00	37	2726	2	0	0	2	0
4AOB_A	SAM links to Rfam database...	0.85	0.79	0.92	23	1412	4	0	2	2	6
4ENB_A	crcB links to Rfam database...	0.61	0.53	0.73	8	461	5	1	2	2	7
4ENC_A	crcB links to Rfam database...	0.61	0.53	0.73	8	485	5	1	2	2	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.87	0.83	0.91	20	1180	3	0	2	1	4
4FRN_A	AdoCbl-variant links to Rfam database...	0.83	0.79	0.88	22	1823	3	2	1	0	6
4JF2_A	preQ1-II links to Rfam database...	0.76	0.63	0.94	15	1066	1	1	0	0	9

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Performance of RNASLOpt - scored lower in this pairwise comparison

1. Total counts & total scores for RNASLOpt

Total Base Pair Counts
Total TP	352
Total TN	51403
Total FP	305
Total FP CONTRA	71
Total FP INCONS	151
Total FP COMP	83
Total FN	256

Total Scores
MCC	0.591
Average MCC ± 95% Confidence Intervals	0.590 ± 0.115
Sensitivity	0.579
Positive Predictive Value	0.613
Nr of predictions	25

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.48	0.39	0.64	7	517	4	0	4	0	11
3J16_L	tRNA links to Rfam database...	0.63	0.57	0.71	12	1142	5	0	5	0	9
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.68	0.74	23	2989	11	0	8	3	11
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2724	30	6	12	12	15
3J3E_7	5S_rRNA links to Rfam database...	0.61	0.56	0.68	19	2713	10	1	8	1	15
3J3F_7	5S_rRNA links to Rfam database...	0.21	0.22	0.22	8	2898	28	3	25	0	28
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.47	0.32	9	4733	38	10	9	19	10
3J3V_B	5S_rRNA links to Rfam database...	0.60	0.59	0.62	16	2630	14	2	8	4	11
3UZL_B	tRNA links to Rfam database...	0.55	0.50	0.62	8	1280	9	1	4	4	8
3W1K_J	tRNA-Sec links to Rfam database...	0.93	0.90	0.97	28	1649	1	1	0	0	3
3W3S_B	tRNA-Sec links to Rfam database...	0.90	0.85	0.97	28	1960	2	0	1	1	5
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.74	1.00	26	2770	4	0	0	4	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.34	0.31	10	5342	36	8	14	14	19
3ZND_W	tRNA links to Rfam database...	0.26	0.38	0.19	3	1175	22	7	6	9	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.30	0.40	0.24	8	4482	35	13	13	9	12
4A1C_3	5S_rRNA links to Rfam database...	0.79	0.73	0.87	27	2732	5	0	4	1	10
4AOB_A	SAM links to Rfam database...	0.31	0.28	0.38	8	1416	13	3	10	0	21
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.19	0.18	0.22	5	1825	18	6	12	0	23
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5

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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 PETfold_pre2.0(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(seed)

2. Individual counts for PETfold_pre2.0(seed) [ download as .csv ]

Performance of RNASLOpt - scored lower in this pairwise comparison

1. Total counts & total scores for RNASLOpt

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