CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Multilign(20)		Murlet(seed)
MCC	0.673	>	0.636
Average MCC ± 95% Confidence Intervals	0.532 ± 0.128	>	0.473 ± 0.136
Sensitivity	0.523	>	0.428
Positive Predictive Value	0.872	<	0.952
Total TP	383	>	314
Total TN	76008	<	76117
Total FP	95	>	18
Total FP CONTRA	9	>	0
Total FP INCONS	47	>	16
Total FP COMP	39	>	2
Total FN	350	<	419
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Multilign(20) and Murlet(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 Multilign(20) and Murlet(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 Multilign(20) and Murlet(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Multilign(20) and Murlet(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 Multilign(20) and Murlet(seed)).

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

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

Total Base Pair Counts
Total TP	383
Total TN	76008
Total FP	95
Total FP CONTRA	9
Total FP INCONS	47
Total FP COMP	39
Total FN	350

Total Scores
MCC	0.673
Average MCC ± 95% Confidence Intervals	0.532 ± 0.128
Sensitivity	0.523
Positive Predictive Value	0.872
Nr of predictions	44

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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
PDB_00012	mir-TAR links to Rfam database...	1.00	1.00	1.00	7	399	3	0	0	3	0
PDB_00213	Gammaretro_CES links to Rfam database...	0.86	0.78	0.94	32	5016	2	0	2	0	9
PDB_00553	mir-TAR links to Rfam database...	1.00	1.00	1.00	11	454	0	0	0	0	0
PDB_00810	s2m links to Rfam database...	0.67	0.59	0.77	10	1068	3	0	3	0	7
PDB_01050	UnaL2 links to Rfam database...	0.92	0.85	1.00	11	619	2	0	0	2	2
PDB_01152	HIV_FS2 links to Rfam database...	0.88	0.79	1.00	11	550	0	0	0	0	3
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	2	0	0	2	0
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00587	Y_RNA links to Rfam database...	0.93	0.93	0.93	14	4836	15	0	1	14	1
RFA_00658	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00664	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00667	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00668	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00672	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	13
RFA_00673	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00674	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00675	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00677	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00678	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	946	0	0	0	0	14
RFA_00680	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00704	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00707	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00715	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	946	0	0	0	0	14
RFA_00717	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	14
RFA_00730	s2m links to Rfam database...	0.69	0.67	0.73	8	892	4	1	2	1	4
RFA_00731	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00733	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00734	s2m links to Rfam database...	0.78	0.75	0.82	9	892	3	0	2	1	3
RFA_00736	s2m links to Rfam database...	0.69	0.67	0.73	8	892	4	1	2	1	4
RFA_00737	s2m links to Rfam database...	0.73	0.67	0.80	8	893	3	0	2	1	4
RFA_00745	s2m links to Rfam database...	0.69	0.67	0.73	8	935	4	1	2	1	4
RFA_00749	s2m links to Rfam database...	0.69	0.67	0.73	8	892	4	1	2	1	4
RFA_00758	s2m links to Rfam database...	0.63	0.58	0.70	7	893	3	1	2	0	5
RFA_00762	s2m links to Rfam database...	0.69	0.67	0.73	8	892	3	0	3	0	4
RFA_00763	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00764	s2m links to Rfam database...	0.69	0.67	0.73	8	892	4	1	2	1	4
RFA_00765	s2m links to Rfam database...	0.91	0.83	1.00	10	893	1	0	0	1	2
RFA_00786	Gammaretro_CES links to Rfam database...	0.64	0.66	0.64	21	5017	12	2	10	0	11
RFA_00791	Gammaretro_CES links to Rfam database...	0.89	0.84	0.93	27	5122	3	0	2	1	5
RFA_00792	Gammaretro_CES links to Rfam database...	0.94	0.94	0.94	30	5018	4	0	2	2	2
RFA_00801	Gammaretro_CES links to Rfam database...	0.81	0.78	0.83	25	5020	6	0	5	1	7
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.65	0.51	0.84	21	6303	4	1	3	0	20
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	36

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

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

Total Base Pair Counts
Total TP	314
Total TN	76117
Total FP	18
Total FP CONTRA	0
Total FP INCONS	16
Total FP COMP	2
Total FN	419

Total Scores
MCC	0.636
Average MCC ± 95% Confidence Intervals	0.473 ± 0.136
Sensitivity	0.428
Positive Predictive Value	0.952
Nr of predictions	44

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_00012	mir-TAR links to Rfam database...	0.65	0.43	1.00	3	403	0	0	0	0	4
PDB_00213	Gammaretro_CES links to Rfam database...	0.73	0.59	0.92	24	5024	2	0	2	0	17
PDB_00553	mir-TAR links to Rfam database...	0.45	0.27	0.75	3	461	1	0	1	0	8
PDB_00810	s2m links to Rfam database...	0.63	0.53	0.75	9	1069	3	0	3	0	8
PDB_01050	UnaL2 links to Rfam database...	0.55	0.31	1.00	4	626	1	0	0	1	9
PDB_01152	HIV_FS2 links to Rfam database...	0.76	0.64	0.90	9	551	1	0	1	0	5
RFA_00390	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
RFA_00416	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1485	0	0	0	0	15
RFA_00433	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
RFA_00587	Y_RNA links to Rfam database...	0.00	0.00	0.00	0	4851	0	0	0	0	15
RFA_00658	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00664	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00667	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00668	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00672	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	13
RFA_00673	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00674	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00675	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00677	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00678	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	946	0	0	0	0	14
RFA_00680	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00704	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00707	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00715	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	946	0	0	0	0	14
RFA_00717	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	14
RFA_00730	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00731	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00733	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00734	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00736	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00737	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00745	s2m links to Rfam database...	1.00	1.00	1.00	12	934	0	0	0	0	0
RFA_00749	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00758	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00762	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00763	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00764	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00765	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00786	Gammaretro_CES links to Rfam database...	0.83	0.75	0.92	24	5024	2	0	2	0	8
RFA_00791	Gammaretro_CES links to Rfam database...	0.83	0.75	0.92	24	5125	2	0	2	0	8
RFA_00792	Gammaretro_CES links to Rfam database...	0.83	0.75	0.92	24	5024	2	0	2	0	8
RFA_00801	Gammaretro_CES links to Rfam database...	0.80	0.72	0.88	23	5024	3	0	3	0	9
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.35	0.12	1.00	5	6323	1	0	0	1	36
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.41	0.17	1.00	6	5454	0	0	0	0	30

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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 Multilign(20) - scored higher in this pairwise comparison

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

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

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

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

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