CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	Multilign(20)		RNASampler(seed)
MCC	0.692	>	0.571
Average MCC ± 95% Confidence Intervals	0.541 ± 0.132	>	0.424 ± 0.109
Sensitivity	0.552	>	0.343
Positive Predictive Value	0.874	<	0.957
Total TP	362	>	225
Total TN	64245	<	64424
Total FP	91	>	25
Total FP CONTRA	8	>	0
Total FP INCONS	44	>	10
Total FP COMP	39	>	15
Total FN	294	<	431
P-value	3.56938820447e-08

^top

Performance plots

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

^top

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

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

Total Base Pair Counts
Total TP	362
Total TN	64245
Total FP	91
Total FP CONTRA	8
Total FP INCONS	44
Total FP COMP	39
Total FN	294

Total Scores
MCC	0.692
Average MCC ± 95% Confidence Intervals	0.541 ± 0.132
Sensitivity	0.552
Positive Predictive Value	0.874
Nr of predictions	42

^top

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

^top

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

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

Total Base Pair Counts
Total TP	225
Total TN	64424
Total FP	25
Total FP CONTRA	0
Total FP INCONS	10
Total FP COMP	15
Total FN	431

Total Scores
MCC	0.571
Average MCC ± 95% Confidence Intervals	0.424 ± 0.109
Sensitivity	0.343
Positive Predictive Value	0.957
Nr of predictions	42

^top

2. Individual counts for RNASampler(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...	1.00	1.00	1.00	7	399	3	0	0	3	0
PDB_00213	Gammaretro_CES links to Rfam database...	0.76	0.59	1.00	24	5026	0	0	0	0	17
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...	0.42	0.18	1.00	3	1078	0	0	0	0	14
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...	0.84	0.71	1.00	10	551	0	0	0	0	4
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...	0.63	0.40	1.00	6	1479	1	0	0	1	9
RFA_00433	Hammerhead_3 links to Rfam database...	0.63	0.40	1.00	6	1425	1	0	0	1	9
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	5	0	0	5	0
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...	0.53	0.29	1.00	4	986	0	0	0	0	10
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...	-0.01	0.00	0.00	0	987	3	0	3	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...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00731	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00733	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00734	s2m links to Rfam database...	0.64	0.42	1.00	5	898	0	0	0	0	7
RFA_00736	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00737	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00745	s2m links to Rfam database...	0.50	0.25	1.00	3	943	0	0	0	0	9
RFA_00749	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00758	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00762	s2m links to Rfam database...	0.64	0.42	1.00	5	898	0	0	0	0	7
RFA_00763	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00764	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00765	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00786	Gammaretro_CES links to Rfam database...	0.79	0.63	1.00	20	5030	0	0	0	0	12
RFA_00791	Gammaretro_CES links to Rfam database...	0.71	0.56	0.90	18	5131	2	0	2	0	14
RFA_00792	Gammaretro_CES links to Rfam database...	0.81	0.72	0.92	23	5025	2	0	2	0	9
RFA_00801	Gammaretro_CES links to Rfam database...	0.74	0.63	0.87	20	5027	4	0	3	1	12

^top

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 RNASampler(seed) - scored lower in this pairwise comparison

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

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