CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	IPknot		Alterna
MCC	0.683	>	0.589
Average MCC ± 95% Confidence Intervals	0.693 ± 0.136	>	0.631 ± 0.142
Sensitivity	0.568	>	0.527
Positive Predictive Value	0.829	>	0.669
Total TP	209	>	194
Total TN	27025	>	26987
Total FP	49	<	107
Total FP CONTRA	7	<	15
Total FP INCONS	36	<	81
Total FP COMP	6	<	11
Total FN	159	<	174
P-value	5.10776592382e-08

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Performance plots

Comparison of performance of IPknot and Alterna. 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 IPknot and Alterna).
Comparison of performance of IPknot and Alterna. 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 IPknot and Alterna).
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 IPknot and Alterna).
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 IPknot and Alterna).
Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and Alterna. 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 IPknot and Alterna).
Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and Alterna. 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 IPknot and Alterna).

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Performance of IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	209
Total TN	27025
Total FP	49
Total FP CONTRA	7
Total FP INCONS	36
Total FP COMP	6
Total FN	159

Total Scores
MCC	0.683
Average MCC ± 95% Confidence Intervals	0.693 ± 0.136
Sensitivity	0.568
Positive Predictive Value	0.829
Nr of predictions	22

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.40	0.30	0.55	6	1529	5	1	4	0	14
2LDL_A	-	0.90	0.82	1.00	9	342	0	0	0	0	2
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2YIE_Z	-	0.43	0.42	0.45	5	1529	6	3	3	0	7
2YIE_X	-	0.67	0.58	0.78	7	1369	3	1	1	1	5
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3J0L_a	-	0.21	0.19	0.25	3	1116	9	1	8	0	13
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_1	-	0.76	0.63	0.92	12	1212	2	0	1	1	7
3J0L_7	-	-0.01	0.00	0.00	0	1218	7	0	7	0	17
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
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...	0.61	0.48	0.80	20	3891	5	0	5	0	22
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3TRZ_Z	-	0.91	0.83	1.00	5	205	1	0	0	1	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17

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Performance of Alterna - scored lower in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP	194
Total TN	26987
Total FP	107
Total FP CONTRA	15
Total FP INCONS	81
Total FP COMP	11
Total FN	174

Total Scores
MCC	0.589
Average MCC ± 95% Confidence Intervals	0.631 ± 0.142
Sensitivity	0.527
Positive Predictive Value	0.669
Nr of predictions	22

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.40	0.53	8	1525	7	0	7	0	12
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
2YIE_X	-	0.36	0.33	0.40	4	1368	9	2	4	3	8
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3J0L_a	-	0.23	0.19	0.30	3	1118	7	1	6	0	13
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_1	-	0.61	0.53	0.71	10	1211	6	0	4	2	9
3J0L_7	-	0.26	0.24	0.31	4	1212	9	0	9	0	13
3J0L_g	-	-0.01	0.00	0.00	0	456	9	4	5	0	4
3J16_L	tRNA links to Rfam database...	0.63	0.53	0.76	16	2754	5	1	4	0	14
3RKF_A	Purine links to Rfam database...	0.69	0.56	0.86	19	2189	3	1	2	0	15
3SD1_A	THF links to Rfam database...	0.46	0.38	0.57	16	3888	12	1	11	0	26
3SIU_F	-	0.59	0.55	0.67	6	369	3	0	3	0	5
3SN2_B	IRE_II links to Rfam database...	0.91	0.83	1.00	10	396	0	0	0	0	2
3TRZ_Z	-	0.91	0.83	1.00	5	205	2	0	0	2	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3UZL_B	tRNA links to Rfam database...	0.52	0.43	0.64	16	3545	9	2	7	0	21

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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 IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

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

Performance of Alterna - scored lower in this pairwise comparison

1. Total counts & total scores for Alterna

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