CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CentroidAlifold(seed)		HotKnots
MCC	0.605	>	0.599
Average MCC ± 95% Confidence Intervals	0.566 ± 0.067	<	0.652 ± 0.081
Sensitivity	0.419	<	0.547
Positive Predictive Value	0.878	>	0.660
Total TP	629	<	821
Total TN	296193	>	295665
Total FP	122	<	494
Total FP CONTRA	14	<	76
Total FP INCONS	73	<	347
Total FP COMP	35	<	71
Total FN	873	>	681
P-value	0.000451186043411

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	629
Total TN	296193
Total FP	122
Total FP CONTRA	14
Total FP INCONS	73
Total FP COMP	35
Total FN	873

Total Scores
MCC	0.605
Average MCC ± 95% Confidence Intervals	0.566 ± 0.067
Sensitivity	0.419
Positive Predictive Value	0.878
Nr of predictions	43

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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	0.42	0.47	8	1111	10	0	9	1	11
2KUR_A	K10_TLS links to Rfam database...	0.77	0.71	0.83	15	1110	3	0	3	0	6
2KUU_A	K10_TLS links to Rfam database...	0.84	0.76	0.94	16	1111	2	0	1	1	5
2KUV_A	K10_TLS links to Rfam database...	0.44	0.41	0.50	9	1110	9	0	9	0	13
2KUW_A	K10_TLS links to Rfam database...	0.45	0.43	0.50	9	1110	9	0	9	0	12
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	861	0	0	0	0	18
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.53	0.50	0.59	10	973	7	0	7	0	10
2LC8_A	GP_knot1 links to Rfam database...	0.00	0.00	0.00	0	1540	0	0	0	0	20
2WRQ_Y	tRNA links to Rfam database...	0.24	0.12	0.50	2	2846	4	0	2	2	15
2WWQ_V	tRNA links to Rfam database...	0.46	0.21	1.00	6	2920	0	0	0	0	22
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.53	0.50	0.56	10	4542	20	0	8	12	10
2XQD_Y	tRNA links to Rfam database...	0.47	0.22	1.00	6	2844	0	0	0	0	21
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.77	0.64	0.93	27	5122	3	0	2	1	15
2ZZM_B	tRNA links to Rfam database...	0.14	0.06	0.33	2	3480	4	0	4	0	30
2ZZN_D	tRNA links to Rfam database...	0.47	0.22	1.00	6	2479	0	0	0	0	21
3A2K_C	tRNA links to Rfam database...	0.46	0.21	1.00	6	2920	0	0	0	0	22
3A3A_A	tRNA-Sec links to Rfam database...	0.85	0.73	1.00	27	3628	0	0	0	0	10
3AKZ_H	tRNA links to Rfam database...	0.46	0.21	1.00	6	2695	0	0	0	0	22
3AMU_B	tRNA links to Rfam database...	0.47	0.22	1.00	6	2997	0	0	0	0	21
3GX2_A	SAM links to Rfam database...	0.77	0.60	1.00	24	4347	1	0	0	1	16
3IVN_B	Purine links to Rfam database...	0.78	0.65	0.95	20	2325	1	1	0	0	11
3IYQ_A	tmRNA links to Rfam database...	0.52	0.39	0.70	37	60673	21	10	6	5	57
3IZ4_A	tmRNA links to Rfam database...	0.58	0.39	0.88	51	70818	7	2	5	0	81
3IZF_C	5S_rRNA links to Rfam database...	0.54	0.30	1.00	16	6887	0	0	0	0	38
3J16_L	tRNA links to Rfam database...	0.45	0.20	1.00	6	2769	0	0	0	0	24
3JYV_7	tRNA links to Rfam database...	0.43	0.19	1.00	6	2844	0	0	0	0	26
3JYX_4	5_8S_rRNA links to Rfam database...	0.52	0.30	0.91	10	12235	3	0	1	2	23
3JYX_3	5S_rRNA links to Rfam database...	0.59	0.41	0.85	11	6315	5	0	2	3	16
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.71	0.54	0.93	25	6994	4	1	1	2	21
3O58_2	5S_rRNA links to Rfam database...	0.65	0.42	1.00	16	7244	0	0	0	0	22
3O58_3	5_8S_rRNA links to Rfam database...	0.56	0.34	0.92	12	12390	1	0	1	0	23
3PDR_A	ykoK links to Rfam database...	0.77	0.61	0.98	44	12835	3	0	1	2	28
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...	0.71	0.52	0.96	22	3893	1	0	1	0	20
3UZL_B	tRNA links to Rfam database...	0.40	0.16	1.00	6	3564	0	0	0	0	31
4A1C_3	5S_rRNA links to Rfam database...	0.54	0.30	1.00	16	7124	0	0	0	0	38
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.24	0.89	8	11772	3	0	1	2	25
4AOB_A	SAM links to Rfam database...	0.75	0.57	1.00	24	4347	1	0	0	1	18
4ENB_A	crcB links to Rfam database...	0.65	0.42	1.00	8	1267	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.65	0.42	1.00	8	1318	0	0	0	0	11

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Performance of HotKnots - scored lower in this pairwise comparison

1. Total counts & total scores for HotKnots

Total Base Pair Counts
Total TP	821
Total TN	295665
Total FP	494
Total FP CONTRA	76
Total FP INCONS	347
Total FP COMP	71
Total FN	681

Total Scores
MCC	0.599
Average MCC ± 95% Confidence Intervals	0.652 ± 0.081
Sensitivity	0.547
Positive Predictive Value	0.660
Nr of predictions	43

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2. Individual counts for HotKnots [ 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...	0.97	0.95	1.00	18	1110	1	0	0	1	1
2KUR_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
2KUU_A	K10_TLS links to Rfam database...	0.92	0.86	1.00	18	1110	1	0	0	1	3
2KUV_A	K10_TLS links to Rfam database...	0.93	0.86	1.00	19	1109	0	0	0	0	3
2KUW_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WWQ_V	tRNA links to Rfam database...	0.76	0.68	0.86	19	2904	5	0	3	2	9
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	23	0	9	14	10
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.34	0.31	0.39	13	5118	20	1	19	0	29
2ZZM_B	tRNA links to Rfam database...	0.21	0.19	0.25	6	3462	18	0	18	0	26
2ZZN_D	tRNA links to Rfam database...	0.82	0.78	0.88	21	2461	3	0	3	0	6
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
3AKZ_H	tRNA links to Rfam database...	0.43	0.39	0.48	11	2678	12	2	10	0	17
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3GX2_A	SAM links to Rfam database...	0.68	0.55	0.85	22	4345	5	0	4	1	18
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IYQ_A	tmRNA links to Rfam database...	0.31	0.34	0.29	32	60617	81	22	55	4	62
3IZ4_A	tmRNA links to Rfam database...	0.51	0.47	0.55	62	70763	52	10	41	1	70
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.61	0.80	33	6862	8	1	7	0	21
3J16_L	tRNA links to Rfam database...	0.26	0.23	0.30	7	2752	16	1	15	0	23
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2828	22	1	21	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.32	0.30	0.33	10	12216	31	5	15	11	23
3JYX_3	5S_rRNA links to Rfam database...	0.62	0.63	0.61	17	6300	22	1	10	11	10
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.78	0.65	0.94	30	6989	5	0	2	3	16
3O58_2	5S_rRNA links to Rfam database...	0.71	0.71	0.71	27	7222	12	4	7	1	11
3O58_3	5_8S_rRNA links to Rfam database...	0.23	0.26	0.21	9	12360	34	10	24	0	26
3PDR_A	ykoK links to Rfam database...	0.67	0.56	0.82	40	12831	11	0	9	2	32
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...	0.64	0.52	0.79	22	3888	6	1	5	0	20
3UZL_B	tRNA links to Rfam database...	0.48	0.38	0.61	14	3547	9	0	9	0	23
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	42	6	25	11	28
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

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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 CentroidAlifold(seed) - scored higher in this pairwise comparison

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

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

Performance of HotKnots - scored lower in this pairwise comparison

1. Total counts & total scores for HotKnots

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