CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAshapes		Alterna
MCC	0.463	>	0.393
Average MCC ± 95% Confidence Intervals	0.524 ± 0.087	>	0.445 ± 0.097
Sensitivity	0.426	>	0.365
Positive Predictive Value	0.515	>	0.435
Total TP	372	>	319
Total TN	76876	>	76865
Total FP	359	<	434
Total FP CONTRA	37	<	40
Total FP INCONS	313	<	374
Total FP COMP	9	<	20
Total FN	501	<	554
P-value	3.56938820447e-08

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Performance plots

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

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Performance of RNAshapes - scored higher in this pairwise comparison

1. Total counts & total scores for RNAshapes

Total Base Pair Counts
Total TP	372
Total TN	76876
Total FP	359
Total FP CONTRA	37
Total FP INCONS	313
Total FP COMP	9
Total FN	501

Total Scores
MCC	0.463
Average MCC ± 95% Confidence Intervals	0.524 ± 0.087
Sensitivity	0.426
Positive Predictive Value	0.515
Nr of predictions	46

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.88	0.79	1.00	11	935	0	0	0	0	3
PDB_00018	-	0.20	0.20	0.22	4	1017	14	2	12	0	16
PDB_00020	-	0.38	0.35	0.44	7	764	9	0	9	0	13
PDB_00041	-	0.70	0.50	1.00	6	624	0	0	0	0	6
PDB_00053	-	0.73	0.55	1.00	6	429	0	0	0	0	5
PDB_00056	-	0.93	0.88	1.00	14	616	0	0	0	0	2
PDB_00123	-	-0.01	0.00	0.00	0	4151	35	0	35	0	36
PDB_00124	-	0.59	0.50	0.71	5	489	2	0	2	0	5
PDB_00128	-	0.80	0.71	0.91	10	485	1	0	1	0	4
PDB_00134	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00138	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00209	-	0.56	0.45	0.71	5	554	2	0	2	0	6
PDB_00243	-	0.63	0.58	0.70	7	620	3	0	3	0	5
PDB_00352	-	0.89	0.79	1.00	15	1210	0	0	0	0	4
PDB_00571	tRNA links to Rfam database...	0.17	0.16	0.19	4	3300	17	6	11	0	21
PDB_00713	-	0.43	0.43	0.45	9	1996	11	0	11	0	12
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2678	24	1	22	1	23
PDB_00828	Purine links to Rfam database...	0.88	0.78	1.00	21	2464	0	0	0	0	6
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_00842	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00851	-	0.35	0.29	0.43	12	4725	16	0	16	0	29
PDB_00857	-	0.54	0.40	0.75	6	1073	2	0	2	0	9
PDB_00874	-	0.10	0.10	0.14	2	932	12	2	10	0	18
PDB_00886	-	-0.01	0.00	0.00	0	4148	38	0	38	0	40
PDB_00918	-	0.75	0.57	1.00	4	321	0	0	0	0	3
PDB_01009	tRNA links to Rfam database...	0.52	0.57	0.48	12	2460	13	5	8	0	9
PDB_01020	Purine links to Rfam database...	0.86	0.74	1.00	17	2261	1	0	0	1	6
PDB_01040	-	0.30	0.30	0.32	6	1109	13	0	13	0	14
PDB_01059	-	0.75	0.57	1.00	4	227	0	0	0	0	3
PDB_01073	SAM links to Rfam database...	0.52	0.47	0.57	16	4343	13	2	10	1	18
PDB_01194	-	-0.02	0.00	0.00	0	488	8	0	8	0	15
PDB_01201	-	0.85	0.73	1.00	16	1112	0	0	0	0	6
PDB_01203	-	0.71	0.63	0.80	12	1161	3	2	1	0	7
PDB_01260	-	0.56	0.48	0.67	12	1812	6	0	6	0	13
PDB_01281	-	-0.03	0.00	0.00	0	366	12	0	12	0	14
PDB_01299	-	0.74	0.67	0.83	10	891	2	1	1	0	5
RFA_00632	HDV_ribozyme links to Rfam database...	0.34	0.36	0.33	10	4065	20	2	18	0	18
RFA_00636	HDV_ribozyme links to Rfam database...	0.42	0.43	0.43	12	3977	16	2	14	0	16
RFA_00767	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	4	0	4	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.48	0.44	0.53	8	1876	7	1	6	0	10
RFA_00769	Corona_pk3 links to Rfam database...	0.54	0.56	0.53	10	1934	9	4	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	2001	8	0	5	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	4	1	0	3	8
RFA_00779	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2001	15	2	13	0	16
RFA_00809	RydC links to Rfam database...	0.36	0.38	0.35	6	2128	11	1	10	0	10

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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	319
Total TN	76865
Total FP	434
Total FP CONTRA	40
Total FP INCONS	374
Total FP COMP	20
Total FN	554

Total Scores
MCC	0.393
Average MCC ± 95% Confidence Intervals	0.445 ± 0.097
Sensitivity	0.365
Positive Predictive Value	0.435
Nr of predictions	46

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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
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.88	0.79	1.00	11	935	0	0	0	0	3
PDB_00018	-	0.20	0.20	0.22	4	1017	14	2	12	0	16
PDB_00020	-	0.38	0.35	0.44	7	764	9	0	9	0	13
PDB_00041	-	0.70	0.50	1.00	6	624	0	0	0	0	6
PDB_00053	-	0.73	0.55	1.00	6	429	0	0	0	0	5
PDB_00056	-	0.11	0.13	0.14	2	616	12	0	12	0	14
PDB_00123	-	-0.01	0.00	0.00	0	4151	35	0	35	0	36
PDB_00124	-	-0.02	0.00	0.00	0	488	8	2	6	0	10
PDB_00128	-	0.80	0.71	0.91	10	485	1	0	1	0	4
PDB_00134	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00138	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00209	-	0.68	0.55	0.86	6	554	1	1	0	0	5
PDB_00243	-	0.51	0.50	0.55	6	619	5	0	5	0	6
PDB_00352	-	0.92	0.84	1.00	16	1209	0	0	0	0	3
PDB_00571	tRNA links to Rfam database...	0.41	0.40	0.43	10	3298	13	3	10	0	15
PDB_00713	-	-0.01	0.00	0.00	0	1997	19	0	19	0	21
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2680	21	3	18	0	23
PDB_00828	Purine links to Rfam database...	0.88	0.78	1.00	21	2464	0	0	0	0	6
PDB_00829	Purine links to Rfam database...	0.77	0.71	0.85	17	2258	3	2	1	0	7
PDB_00842	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00851	-	0.10	0.10	0.13	4	4721	28	0	28	0	37
PDB_00857	-	-0.01	0.00	0.00	0	1068	13	0	13	0	15
PDB_00874	-	0.09	0.10	0.11	2	928	16	2	14	0	18
PDB_00886	-	-0.01	0.00	0.00	0	4148	38	0	38	0	40
PDB_00918	-	0.75	0.57	1.00	4	321	0	0	0	0	3
PDB_01009	tRNA links to Rfam database...	0.86	0.86	0.86	18	2464	6	0	3	3	3
PDB_01020	Purine links to Rfam database...	0.76	0.70	0.84	16	2259	4	2	1	1	7
PDB_01040	-	0.30	0.30	0.32	6	1109	13	0	13	0	14
PDB_01059	-	0.49	0.43	0.60	3	226	2	2	0	0	4
PDB_01073	SAM links to Rfam database...	0.52	0.47	0.57	16	4343	13	2	10	1	18
PDB_01194	-	-0.02	0.00	0.00	0	488	8	0	8	0	15
PDB_01201	-	0.85	0.73	1.00	16	1112	0	0	0	0	6
PDB_01203	-	0.74	0.68	0.81	13	1160	3	2	1	0	6
PDB_01260	-	-0.01	0.00	0.00	0	1809	21	0	21	0	25
PDB_01281	-	-0.03	0.00	0.00	0	366	12	0	12	0	14
PDB_01299	-	0.74	0.67	0.83	10	891	2	1	1	0	5
RFA_00632	HDV_ribozyme links to Rfam database...	0.24	0.25	0.23	7	4065	23	3	20	0	21
RFA_00636	HDV_ribozyme links to Rfam database...	0.50	0.46	0.54	13	3981	13	3	8	2	15
RFA_00767	Corona_pk3 links to Rfam database...	0.54	0.50	0.60	9	1876	6	2	4	0	9
RFA_00768	Corona_pk3 links to Rfam database...	0.50	0.44	0.57	8	1877	9	0	6	3	10
RFA_00769	Corona_pk3 links to Rfam database...	0.38	0.39	0.39	7	1935	11	2	9	0	11
RFA_00770	Corona_pk3 links to Rfam database...	0.45	0.39	0.54	7	2003	9	0	6	3	11
RFA_00773	Corona_pk3 links to Rfam database...	0.45	0.39	0.54	7	1940	9	0	6	3	11
RFA_00779	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1939	4	3	1	0	8
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	1999	19	3	14	2	16
RFA_00809	RydC links to Rfam database...	0.38	0.38	0.40	6	2130	11	0	9	2	10

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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 RNAshapes - scored higher in this pairwise comparison

1. Total counts & total scores for RNAshapes

2. Individual counts for RNAshapes [ 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 ]