CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Pknots		CentroidAlifold(seed)
MCC	0.717	>	0.711
Average MCC ± 95% Confidence Intervals	0.750 ± 0.096	>	0.643 ± 0.080
Sensitivity	0.748	>	0.564
Positive Predictive Value	0.695	<	0.904
Total TP	687	>	518
Total TN	62073	<	62488
Total FP	420	>	117
Total FP CONTRA	101	>	5
Total FP INCONS	200	>	50
Total FP COMP	119	>	62
Total FN	231	<	400
P-value	0.103865234064

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Performance plots

Comparison of performance of Pknots and CentroidAlifold(seed). 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 Pknots and CentroidAlifold(seed)).
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 Pknots and CentroidAlifold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Pknots and CentroidAlifold(seed). 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 Pknots and CentroidAlifold(seed)).

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Performance of Pknots - scored higher in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	687
Total TN	62073
Total FP	420
Total FP CONTRA	101
Total FP INCONS	200
Total FP COMP	119
Total FN	231

Total Scores
MCC	0.717
Average MCC ± 95% Confidence Intervals	0.750 ± 0.096
Sensitivity	0.748
Positive Predictive Value	0.695
Nr of predictions	41

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	449	1	0	0	1	0
2KUR_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	448	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	429	1	0	0	1	0
2KUV_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	420	0	0	0	0	0
2KUW_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	452	1	0	0	1	0
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	0	0	0	0	0
2L1F_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	0.94	0.94	0.94	17	339	2	0	1	1	1
2LC8_A	GP_knot1 links to Rfam database...	0.83	0.83	0.83	15	510	3	2	1	0	3
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	13	0	0	13	0
2WWQ_V	tRNA links to Rfam database...	0.29	0.32	0.29	6	1183	16	3	12	1	13
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.21	0.27	0.17	3	1817	33	3	12	18	8
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...	0.32	0.34	0.32	12	2008	26	1	24	1	23
2ZZM_B	tRNA links to Rfam database...	0.18	0.20	0.19	3	1342	23	4	9	10	12
2ZZN_D	tRNA links to Rfam database...	0.95	0.95	0.95	21	962	1	1	0	0	1
3A2K_C	tRNA links to Rfam database...	0.50	0.55	0.48	12	1083	13	3	10	0	10
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3AKZ_H	tRNA links to Rfam database...	1.00	1.00	1.00	20	1107	2	0	0	2	0
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	3	0	0	3	0
3GX2_A	SAM links to Rfam database...	0.55	0.57	0.55	16	1420	14	4	9	1	12
3IVN_B	Purine links to Rfam database...	0.91	0.87	0.95	20	882	1	0	1	0	3
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	9	0	5	4	3
3J16_L	tRNA links to Rfam database...	0.41	0.43	0.41	9	1137	13	1	12	0	12
3JYV_7	tRNA links to Rfam database...	0.97	0.95	1.00	19	1092	2	0	0	2	1
3JYX_4	5_8S_rRNA links to Rfam database...	0.33	0.58	0.19	7	4720	41	22	7	12	5
3JYX_3	5S_rRNA links to Rfam database...	0.37	0.53	0.27	8	2348	26	17	5	4	7
3LA5_A	Purine links to Rfam database...	0.94	0.88	1.00	22	932	0	0	0	0	3
3NPB_A	SAM links to Rfam database...	0.84	0.81	0.88	30	2244	9	0	4	5	7
3O58_2	5S_rRNA links to Rfam database...	0.93	0.90	0.97	28	2725	3	0	1	2	3
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.45	0.24	10	4722	39	18	14	7	12
3PDR_A	ykoK links to Rfam database...	0.64	0.64	0.65	32	4791	19	4	13	2	18
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.78	0.76	0.81	22	1506	5	1	4	0	7
3UZL_B	tRNA links to Rfam database...	1.00	1.00	1.00	16	1277	7	0	0	7	0
4A1C_3	5S_rRNA links to Rfam database...	0.28	0.30	0.28	11	2723	30	4	25	1	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.29	8	4488	36	9	11	16	12
4AOB_A	SAM links to Rfam database...	0.19	0.21	0.21	6	1409	23	3	19	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	2	0	0	2	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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Performance of CentroidAlifold(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidAlifold(seed)

Total Base Pair Counts
Total TP	518
Total TN	62488
Total FP	117
Total FP CONTRA	5
Total FP INCONS	50
Total FP COMP	62
Total FN	400

Total Scores
MCC	0.711
Average MCC ± 95% Confidence Intervals	0.643 ± 0.080
Sensitivity	0.564
Positive Predictive Value	0.904
Nr of predictions	41

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KE6_A	K10_TLS links to Rfam database...	0.44	0.44	0.47	8	450	10	0	9	1	10
2KUR_A	K10_TLS links to Rfam database...	0.77	0.74	0.82	14	450	4	0	3	1	5
2KUU_A	K10_TLS links to Rfam database...	0.88	0.83	0.94	15	431	3	0	1	2	3
2KUV_A	K10_TLS links to Rfam database...	0.46	0.47	0.50	9	421	9	0	9	0	10
2KUW_A	K10_TLS links to Rfam database...	0.44	0.44	0.47	8	453	10	0	9	1	10
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	371	0	0	0	0	16
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	0	0	0	0	0
2L1F_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	0.51	0.50	0.56	9	341	8	0	7	1	9
2LC8_A	GP_knot1 links to Rfam database...	0.00	0.00	0.00	0	528	0	0	0	0	18
2WRQ_Y	tRNA links to Rfam database...	0.47	0.22	1.00	2	1150	4	0	0	4	7
2WWQ_V	tRNA links to Rfam database...	0.56	0.32	1.00	6	1198	0	0	0	0	13
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.67	0.73	0.62	8	1822	22	0	5	17	3
2XQD_Y	tRNA links to Rfam database...	0.48	0.24	1.00	5	1124	1	0	0	1	16
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.83	0.74	0.93	26	2017	4	0	2	2	9
2ZZM_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	1358	6	0	0	6	15
2ZZN_D	tRNA links to Rfam database...	0.52	0.27	1.00	6	978	0	0	0	0	16
3A2K_C	tRNA links to Rfam database...	0.52	0.27	1.00	6	1102	0	0	0	0	16
3A3A_A	tRNA-Sec links to Rfam database...	0.95	0.90	1.00	27	1473	0	0	0	0	3
3AKZ_H	tRNA links to Rfam database...	0.50	0.25	1.00	5	1122	1	0	0	1	15
3AMU_B	tRNA links to Rfam database...	0.51	0.26	1.00	5	1152	1	0	0	1	14
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	0.83	0.90	19	882	2	2	0	0	4
3IZF_C	5S_rRNA links to Rfam database...	0.67	0.46	1.00	16	2624	0	0	0	0	19
3J16_L	tRNA links to Rfam database...	0.53	0.29	1.00	6	1153	0	0	0	0	15
3JYV_7	tRNA links to Rfam database...	0.50	0.25	1.00	5	1106	1	0	0	1	15
3JYX_4	5_8S_rRNA links to Rfam database...	0.91	0.83	1.00	10	4746	3	0	0	3	2
3JYX_3	5S_rRNA links to Rfam database...	0.65	0.53	0.80	8	2368	8	0	2	6	7
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...	0.79	0.65	0.96	24	2253	5	0	1	4	13
3O58_2	5S_rRNA links to Rfam database...	0.72	0.52	1.00	16	2738	0	0	0	0	15
3O58_3	5_8S_rRNA links to Rfam database...	0.68	0.50	0.92	11	4752	2	1	0	1	11
3PDR_A	ykoK links to Rfam database...	0.93	0.88	0.98	44	4795	3	0	1	2	6
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...	0.85	0.76	0.96	22	1510	1	0	1	0	7
3UZL_B	tRNA links to Rfam database...	0.50	0.25	1.00	4	1289	2	0	0	2	12
4A1C_3	5S_rRNA links to Rfam database...	0.66	0.43	1.00	16	2747	0	0	0	0	21
4A1C_2	5_8S_rRNA links to Rfam database...	0.60	0.40	0.89	8	4507	3	1	0	2	12
4AOB_A	SAM links to Rfam database...	0.89	0.79	1.00	23	1414	2	0	0	2	6
4ENB_A	crcB links to Rfam database...	0.72	0.53	1.00	8	464	0	0	0	0	7
4ENC_A	crcB links to Rfam database...	0.73	0.53	1.00	8	488	0	0	0	0	7

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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 Pknots - scored higher in this pairwise comparison

1. Total counts & total scores for Pknots

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

Performance of CentroidAlifold(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidAlifold(seed)

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