CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAfold		RNAalifold(seed)
MCC	0.620	>	0.593
Average MCC ± 95% Confidence Intervals	0.698 ± 0.098	>	0.597 ± 0.088
Sensitivity	0.568	>	0.397
Positive Predictive Value	0.680	<	0.887
Total TP	583	>	408
Total TN	236405	<	236802
Total FP	334	>	68
Total FP CONTRA	53	>	12
Total FP INCONS	221	>	40
Total FP COMP	60	>	16
Total FN	444	<	619
P-value	5.06544643719e-08

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Performance plots

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Performance of RNAfold - scored higher in this pairwise comparison

1. Total counts & total scores for RNAfold

Total Base Pair Counts
Total TP	583
Total TN	236405
Total FP	334
Total FP CONTRA	53
Total FP INCONS	221
Total FP COMP	60
Total FN	444

Total Scores
MCC	0.620
Average MCC ± 95% Confidence Intervals	0.698 ± 0.098
Sensitivity	0.568
Positive Predictive Value	0.680
Nr of predictions	29

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2. Individual counts for RNAfold [ 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	60616	80	24	54	2	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...	0.31	0.30	0.32	10	12215	33	5	16	12	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...	0.83	0.72	0.97	33	6987	4	0	1	3	13
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	34	2	21	11	23
3PDR_A	ykoK links to Rfam database...	0.75	0.63	0.90	45	12830	7	1	4	2	27
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11744	43	5	27	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...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1314	7	1	6	0	14

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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	408
Total TN	236802
Total FP	68
Total FP CONTRA	12
Total FP INCONS	40
Total FP COMP	16
Total FN	619

Total Scores
MCC	0.593
Average MCC ± 95% Confidence Intervals	0.597 ± 0.088
Sensitivity	0.397
Positive Predictive Value	0.887
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...	0.52	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
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

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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 RNAfold - scored higher in this pairwise comparison

1. Total counts & total scores for RNAfold

2. Individual counts for RNAfold [ 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 ]