CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Sfold		PknotsRG
MCC	0.515	>	0.481
Average MCC ± 95% Confidence Intervals	0.594 ± 0.079	<	0.614 ± 0.084
Sensitivity	0.517	<	0.523
Positive Predictive Value	0.513	>	0.442
Total TP	1765	<	1786
Total TN	5428329	>	5427726
Total FP	2138	<	2725
Total FP CONTRA	476	<	669
Total FP INCONS	1197	<	1586
Total FP COMP	465	<	470
Total FN	1648	>	1627
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Sfold and PknotsRG. 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 Sfold and PknotsRG).
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 Sfold and PknotsRG).
Comparison of average Matthews Correlation Coefficients (MCCs) for Sfold and PknotsRG. 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 Sfold and PknotsRG).

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Performance of Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP	1765
Total TN	5428329
Total FP	2138
Total FP CONTRA	476
Total FP INCONS	1197
Total FP COMP	465
Total FN	1648

Total Scores
MCC	0.515
Average MCC ± 95% Confidence Intervals	0.594 ± 0.079
Sensitivity	0.517
Positive Predictive Value	0.513
Nr of predictions	45

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	-0.03	0.00	0.00	0	229	7	1	6	0	8
2KRL_A	-	0.91	0.87	0.95	20	2003	9	1	0	8	3
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.39	0.58	7	516	5	0	5	0	11
2M58_A	-	0.34	0.25	0.50	3	538	3	1	2	0	9
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2WDL_A	-	0.50	0.50	0.50	392	1444543	429	62	325	42	396
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	3	2	0	1	1
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.67	0.64	0.72	21	1790	9	0	8	1	12
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.86	0.79	0.96	22	1426	2	1	0	1	6
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.69	0.68	0.70	19	1445	9	1	7	1	9
3IYQ_A	tmRNA links to Rfam database...	0.25	0.33	0.19	17	22350	86	39	34	13	34
3IZ4_A	tmRNA links to Rfam database...	0.59	0.56	0.63	53	25452	34	14	17	3	42
3J0L_a	-	0.55	0.64	0.50	7	397	8	5	2	1	4
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J3D_C	tRNA links to Rfam database...	0.44	0.37	0.54	7	955	6	1	5	0	12
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.08	2	2718	32	6	16	10	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.47	0.33	9	4734	37	8	10	19	10
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1095	16	2	14	0	20
3JYX_5	-	0.42	0.46	0.38	223	1968418	588	172	189	227	258
3KIY_A	-	0.53	0.51	0.56	403	1485155	373	56	266	51	383
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.75	0.74	0.78	14	717	4	0	4	0	5
3NPB_A	SAM links to Rfam database...	0.85	0.78	0.94	29	2247	7	0	2	5	8
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.50	0.52	11	4743	18	2	8	8	11
3PDR_A	ykoK links to Rfam database...	0.82	0.80	0.85	40	4793	9	2	5	2	10
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.78	0.72	0.84	21	1508	4	2	2	0	8
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.63	0.64	0.64	21	1956	13	4	8	1	12
3ZEX_B	-	0.37	0.39	0.35	136	420960	296	65	191	40	210
3ZEX_C	5_8S_rRNA links to Rfam database...	0.41	0.34	0.50	10	5354	27	2	8	17	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	34	8	14	12	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ATO_G	-	0.37	0.14	1.00	1	219	0	0	0	0	6
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...	0.57	0.33	1.00	5	491	0	0	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.67	0.58	0.78	14	1184	4	3	1	0	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.71	0.57	0.89	16	1830	2	2	0	0	12
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5
4JRC_A	-	0.34	0.35	0.35	6	605	11	0	11	0	11

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Performance of PknotsRG - scored lower in this pairwise comparison

1. Total counts & total scores for PknotsRG

Total Base Pair Counts
Total TP	1786
Total TN	5427726
Total FP	2725
Total FP CONTRA	669
Total FP INCONS	1586
Total FP COMP	470
Total FN	1627

Total Scores
MCC	0.481
Average MCC ± 95% Confidence Intervals	0.614 ± 0.084
Sensitivity	0.523
Positive Predictive Value	0.442
Nr of predictions	45

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	0.77	0.88	0.70	7	226	3	2	1	0	1
2KRL_A	-	0.85	0.87	0.83	20	2000	12	4	0	8	3
2LC8_A	GP_knot1 links to Rfam database...	0.66	0.61	0.73	11	513	4	2	2	0	7
2M58_A	-	0.96	1.00	0.92	12	531	1	1	0	0	0
2RP0_A	-	0.87	1.00	0.78	7	107	2	2	0	0	0
2WDL_A	-	0.47	0.49	0.45	389	1444457	514	87	389	38	399
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	2	2	0	0	1
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.35	0.36	0.36	12	1786	21	1	20	0	21
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.80	0.79	0.81	22	1422	6	2	3	1	6
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.21	0.21	0.24	6	1447	19	1	18	0	22
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.17	17	22340	94	45	38	11	34
3IZ4_A	tmRNA links to Rfam database...	0.56	0.60	0.52	57	25426	57	25	28	4	38
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J3D_C	tRNA links to Rfam database...	0.63	0.68	0.59	13	946	9	3	6	0	6
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.33	0.21	5	2718	30	6	13	11	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.32	0.42	0.24	8	4728	40	12	13	15	11
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1089	22	4	18	0	20
3JYX_5	-	0.37	0.46	0.29	220	1968248	778	241	293	244	261
3KIY_A	-	0.47	0.50	0.45	393	1485010	525	91	386	48	393
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.93	0.86	1.00	32	2246	4	0	0	4	5
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	35	6	15	14	11
3PDR_A	ykoK links to Rfam database...	0.90	0.90	0.90	45	4790	7	2	3	2	5
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.73	0.72	0.75	21	1505	7	4	3	0	8
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.64	0.64	0.66	21	1957	12	4	7	1	12
3ZEX_B	-	0.36	0.40	0.33	140	420927	323	78	207	38	206
3ZEX_C	5_8S_rRNA links to Rfam database...	0.30	0.34	0.26	10	5336	44	5	23	16	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	43	11	20	12	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ATO_G	-	0.88	1.00	0.78	7	211	2	2	0	0	0
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.59	0.57	0.62	16	1822	10	2	8	0	12
4JF2_A	preQ1-II links to Rfam database...	0.88	0.92	0.85	22	1056	4	4	0	0	2
4JRC_A	-	0.34	0.35	0.35	6	605	11	0	11	0	11

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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 Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

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

Performance of PknotsRG - scored lower in this pairwise comparison

1. Total counts & total scores for PknotsRG

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