CompaRNA - on-line benchmarks of RNA structure prediction methods

CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Table of contents:

Overview

Performance Plots

Performance of Multilign(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Pknots - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for Multilign(20) & Pknots [.zip] - may take several seconds...

Overview

Metric	Multilign(20)		Pknots
MCC	0.521	>	0.507
Average MCC ± 95% Confidence Intervals	0.526 ± 0.210	<	0.587 ± 0.218
Sensitivity	0.428	<	0.452
Positive Predictive Value	0.643	>	0.577
Total TP	142	<	150
Total TN	40943	>	40904
Total FP	86	<	125
Total FP CONTRA	8	=	8
Total FP INCONS	71	<	102
Total FP COMP	7	<	15
Total FN	190	>	182
P-value	9.63256991408e-05

Performance plots

Performance of Multilign(20) - scored higher in this pairwise comparison

1. Total counts & total scores for Multilign(20)

Total Base Pair Counts
Total TP	142
Total TN	40943
Total FP	86
Total FP CONTRA	8
Total FP INCONS	71
Total FP COMP	7
Total FN	190

Total Scores
MCC	0.521
Average MCC ± 95% Confidence Intervals	0.526 ± 0.210
Sensitivity	0.428
Positive Predictive Value	0.643
Nr of predictions	10

2. Individual counts for Multilign(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5139	12	1	11	0	42
3AMU_B	tRNA links to Rfam database...	0.63	0.56	0.71	15	2982	8	0	6	2	12
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.57	0.48	0.69	20	3887	9	1	8	0	22
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	6	0	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11747	33	3	26	4	28
4AOB_A	SAM links to Rfam database...	0.49	0.38	0.64	16	4346	10	1	8	1	26
4ENB_A	crcB links to Rfam database...	0.34	0.26	0.45	5	1264	6	1	5	0	14
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Performance of Pknots - scored lower in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	150
Total TN	40904
Total FP	125
Total FP CONTRA	8
Total FP INCONS	102
Total FP COMP	15
Total FN	182

Total Scores
MCC	0.507
Average MCC ± 95% Confidence Intervals	0.587 ± 0.218
Sensitivity	0.452
Positive Predictive Value	0.577
Nr of predictions	10

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
2L94_A	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.32	0.31	0.34	13	5113	25	1	24	0	29
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	2	0	0	2	7
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.65	0.52	0.81	22	3889	5	0	5	0	20
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.24	0.25	8	11749	36	3	21	12	25
4AOB_A	SAM links to Rfam database...	0.17	0.14	0.21	6	4343	23	1	21	1	36
4ENB_A	crcB links to Rfam database...	0.83	0.79	0.88	15	1258	2	1	1	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.