CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	HotKnots		RNAalifold(seed)
MCC	0.704	>	0.676
Average MCC ± 95% Confidence Intervals	0.793 ± 0.099	>	0.673 ± 0.097
Sensitivity	0.743	>	0.525
Positive Predictive Value	0.673	<	0.874
Total TP	559	>	395
Total TN	87063	<	87442
Total FP	356	>	81
Total FP CONTRA	126	>	25
Total FP INCONS	146	>	32
Total FP COMP	84	>	24
Total FN	193	<	357
P-value	5.23657817852e-08

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Performance plots

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

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Performance of HotKnots - scored higher in this pairwise comparison

1. Total counts & total scores for HotKnots

Total Base Pair Counts
Total TP	559
Total TN	87063
Total FP	356
Total FP CONTRA	126
Total FP INCONS	146
Total FP COMP	84
Total FN	193

Total Scores
MCC	0.704
Average MCC ± 95% Confidence Intervals	0.793 ± 0.099
Sensitivity	0.743
Positive Predictive Value	0.673
Nr of predictions	29

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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...	1.00	1.00	1.00	10	164	0	0	0	0	0
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_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	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
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	0	5	0	7
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	25	0	6	19	3
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.35	0.34	0.38	12	2013	21	1	19	1	23
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.81	0.79	0.85	22	1423	5	2	2	1	6
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.17	17	22341	96	47	35	14	34
3IZ4_A	tmRNA links to Rfam database...	0.56	0.60	0.52	57	25426	57	26	27	4	38
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	31	10	2	19	2
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NPB_A	SAM links to Rfam database...	0.85	0.78	0.94	29	2247	6	0	2	4	8
3O58_3	5_8S_rRNA links to Rfam database...	0.26	0.36	0.19	8	4722	35	16	18	1	14
3PDR_A	ykoK links to Rfam database...	0.81	0.80	0.82	40	4791	11	3	6	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...	0.77	0.76	0.79	22	1505	6	4	2	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	42	12	16	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
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

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

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

Total Base Pair Counts
Total TP	395
Total TN	87442
Total FP	81
Total FP CONTRA	25
Total FP INCONS	32
Total FP COMP	24
Total FN	357

Total Scores
MCC	0.676
Average MCC ± 95% Confidence Intervals	0.673 ± 0.097
Sensitivity	0.525
Positive Predictive Value	0.874
Nr of predictions	29

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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...	0.54	0.30	1.00	3	171	0	0	0	0	7
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...	0.88	0.83	0.94	15	454	2	0	1	1	3
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	371	0	0	0	0	16
2L1F_A	Gammaretro_CES links to Rfam database...	0.68	0.61	0.78	14	745	4	0	4	0	9
2L1F_B	Gammaretro_CES links to Rfam database...	0.65	0.58	0.74	14	772	5	0	5	0	10
2L94_A	HIV_FE links to Rfam database...	0.57	0.39	0.88	7	349	2	0	1	1	11
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	516	12	0	12	0	18
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.80	0.64	1.00	7	1828	2	0	0	2	4
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.50	0.26	1.00	9	2036	0	0	0	0	26
3A3A_A	tRNA-Sec links to Rfam database...	0.79	0.63	1.00	19	1481	0	0	0	0	11
3GX2_A	SAM links to Rfam database...	0.88	0.79	1.00	22	1427	1	0	0	1	6
3IVN_B	Purine links to Rfam database...	0.71	0.65	0.79	15	884	4	2	2	0	8
3IYQ_A	tmRNA links to Rfam database...	0.36	0.27	0.48	14	22411	19	13	2	4	37
3IZ4_A	tmRNA links to Rfam database...	0.46	0.26	0.81	25	25505	8	6	0	2	70
3JYX_4	5_8S_rRNA links to Rfam database...	0.76	0.58	1.00	7	4749	2	0	0	2	5
3LA5_A	Purine links to Rfam database...	0.73	0.64	0.84	16	935	3	1	2	0	9
3NPB_A	SAM links to Rfam database...	0.77	0.59	1.00	22	2256	3	0	0	3	15
3O58_3	5_8S_rRNA links to Rfam database...	0.60	0.36	1.00	8	4756	1	0	0	1	14
3PDR_A	ykoK links to Rfam database...	0.81	0.66	1.00	33	4807	1	0	0	1	17
3RKF_A	Purine links to Rfam database...	0.74	0.67	0.84	16	847	3	1	2	0	8
3SD1_A	THF links to Rfam database...	0.70	0.59	0.85	17	1513	3	2	1	0	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.50	0.25	1.00	5	4511	2	0	0	2	15
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
4ENB_A	crcB links to Rfam database...	0.63	0.40	1.00	6	466	0	0	0	0	9
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9

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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 HotKnots - scored higher in this pairwise comparison

1. Total counts & total scores for HotKnots

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

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

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

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