CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAalifold(seed)		HotKnots
MCC	0.596	>	0.579
Average MCC ± 95% Confidence Intervals	0.601 ± 0.079	<	0.671 ± 0.099
Sensitivity	0.397	<	0.532
Positive Predictive Value	0.897	>	0.635
Total TP	471	<	631
Total TN	264323	>	263854
Total FP	71	<	414
Total FP CONTRA	13	<	67
Total FP INCONS	41	<	296
Total FP COMP	17	<	51
Total FN	716	>	556
P-value	1.97386617324e-07

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	471
Total TN	264323
Total FP	71
Total FP CONTRA	13
Total FP INCONS	41
Total FP COMP	17
Total FN	716

Total Scores
MCC	0.596
Average MCC ± 95% Confidence Intervals	0.601 ± 0.079
Sensitivity	0.397
Positive Predictive Value	0.897
Nr of predictions	33

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.52	0.27	1.00	3	403	0	0	0	0	8
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...	0.84	0.76	0.94	16	1111	1	0	1	0	5
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	861	0	0	0	0	18
2L1F_A	Gammaretro_CES links to Rfam database...	0.67	0.58	0.78	14	2062	4	0	4	0	10
2L1F_B	Gammaretro_CES links to Rfam database...	0.64	0.56	0.74	14	2126	5	0	5	0	11
2L94_A	HIV_FE links to Rfam database...	0.59	0.40	0.89	8	981	1	0	1	0	12
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1528	12	0	12	0	20
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.59	0.35	1.00	7	4553	2	0	0	2	13
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.46	0.21	1.00	9	5142	0	0	0	0	33
3A3A_A	tRNA-Sec links to Rfam database...	0.71	0.51	1.00	19	3636	0	0	0	0	18
3GX2_A	SAM links to Rfam database...	0.74	0.55	1.00	22	4349	1	0	0	1	18
3IVN_B	Purine links to Rfam database...	0.61	0.48	0.79	15	2327	4	2	2	0	16
3IYQ_A	tmRNA links to Rfam database...	0.38	0.21	0.69	20	60697	13	5	4	4	74
3IZ4_A	tmRNA links to Rfam database...	0.42	0.21	0.85	28	70843	5	1	4	0	104
3JYX_4	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	12239	2	0	0	2	26
3LA5_A	Purine links to Rfam database...	0.63	0.47	0.84	16	2466	3	1	2	0	18
3NPB_A	SAM links to Rfam database...	0.66	0.48	0.92	22	6997	3	1	1	1	24
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.26	1.00	9	12394	0	0	0	0	26
3PDR_A	ykoK links to Rfam database...	0.68	0.46	1.00	33	12847	1	0	0	1	39
3RKF_A	Purine links to Rfam database...	0.63	0.47	0.84	16	2192	3	1	2	0	18
3SD1_A	THF links to Rfam database...	0.58	0.40	0.85	17	3896	3	1	2	0	25
3W3S_B	tRNA-Sec links to Rfam database...	0.67	0.45	1.00	18	4735	1	0	0	1	22
3ZEX_C	5_8S_rRNA links to Rfam database...	0.42	0.17	1.00	9	14187	0	0	0	0	43
4A1C_2	5_8S_rRNA links to Rfam database...	0.39	0.15	1.00	5	11776	2	0	0	2	28
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13
4FRG_B	AdoCbl-variant links to Rfam database...	0.73	0.53	1.00	17	3469	0	0	0	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.69	0.53	0.90	19	5130	2	1	1	0	17

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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	631
Total TN	263854
Total FP	414
Total FP CONTRA	67
Total FP INCONS	296
Total FP COMP	51
Total FN	556

Total Scores
MCC	0.579
Average MCC ± 95% Confidence Intervals	0.671 ± 0.099
Sensitivity	0.532
Positive Predictive Value	0.635
Nr of predictions	33

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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
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
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_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	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
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	23	0	9	14	10
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.34	0.31	0.39	13	5118	20	1	19	0	29
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
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
3JYX_4	5_8S_rRNA links to Rfam database...	0.32	0.30	0.33	10	12216	31	5	15	11	23
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_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
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.50	0.61	20	4720	14	1	12	1	20
3ZEX_C	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	14150	46	6	40	0	52
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.32	0.28	0.38	9	3462	15	0	15	0	23
4FRN_A	AdoCbl-variant links to Rfam database...	0.52	0.44	0.62	16	5125	10	2	8	0	20

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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 RNAalifold(seed) - scored higher in this pairwise comparison

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

2. Individual counts for RNAalifold(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 ]