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		Contrafold
MCC	0.737	>	0.734
Average MCC ± 95% Confidence Intervals	0.781 ± 0.051	<	0.784 ± 0.049
Sensitivity	0.761	>	0.755
Positive Predictive Value	0.719	<	0.720
Total TP	1922	>	1906
Total TN	231747	<	231774
Total FP	1102	>	1075
Total FP CONTRA	258	<	263
Total FP INCONS	495	>	479
Total FP COMP	349	>	333
Total FN	602	<	618
P-value	0.00385390231177

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Performance plots

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

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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	1922
Total TN	231747
Total FP	1102
Total FP CONTRA	258
Total FP INCONS	495
Total FP COMP	349
Total FN	602

Total Scores
MCC	0.737
Average MCC ± 95% Confidence Intervals	0.781 ± 0.051
Sensitivity	0.761
Positive Predictive Value	0.719
Nr of predictions	135

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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
2K5Z_A	-	1.00	1.00	1.00	11	175	0	0	0	0	0
2K63_A	-	1.00	1.00	1.00	9	159	0	0	0	0	0
2K66_A	-	1.00	1.00	1.00	9	80	0	0	0	0	0
2KD8_A	-	1.00	1.00	1.00	9	99	0	0	0	0	0
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
2KEZ_A	-	1.00	1.00	1.00	8	94	0	0	0	0	0
2KFC_A	-	-0.03	0.00	0.00	0	229	7	1	6	0	8
2KGP_A	-	1.00	1.00	1.00	9	112	1	0	0	1	0
2KMJ_A	-	1.00	1.00	1.00	11	157	0	0	0	0	0
2KPV_A	-	0.96	0.92	1.00	12	201	0	0	0	0	1
2KRL_A	-	0.91	0.87	0.95	20	2003	9	1	0	8	3
2KU0_A	-	0.96	0.92	1.00	11	281	0	0	0	0	1
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
2KXM_A	-	1.00	1.00	1.00	8	141	0	0	0	0	0
2KZL_A	-	1.00	1.00	1.00	13	507	1	0	0	1	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	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
2L2K_A	-	1.00	1.00	1.00	17	332	0	0	0	0	0
2L3C_B	-	1.00	1.00	1.00	14	225	0	0	0	0	0
2L3E_A	-	1.00	1.00	1.00	12	228	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	1.00	1.00	1.00	30	955	0	0	0	0	0
2L5Z_A	-	1.00	1.00	1.00	9	102	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
2LA5_A	-	0.77	0.71	0.83	5	269	3	0	1	2	2
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	0	5	0	7
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	1.00	1.00	1.00	29	2411	8	0	0	8	0
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2RPT_A	-	1.00	1.00	1.00	7	65	0	0	0	0	0
2RRC_A	-	1.00	1.00	1.00	7	68	0	0	0	0	0
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2WW9_E	-	0.89	0.80	1.00	4	168	0	0	0	0	1
2WW9_D	-	0.08	0.10	0.08	1	729	15	2	9	4	9
2WW9_F	-	0.68	0.75	0.67	6	103	4	1	2	1	2
2WWQ_V	tRNA links to Rfam database...	1.00	1.00	1.00	19	1185	5	0	0	5	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	25	0	6	19	3
2XQD_Y	tRNA links to Rfam database...	0.98	0.95	1.00	20	1109	1	0	0	1	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.35	0.34	0.38	12	2013	21	1	19	1	23
2Y8W_B	-	1.00	1.00	1.00	6	82	1	0	0	1	0
2Y9C_V	-	0.79	0.83	0.75	15	886	8	0	5	3	3
2YIE_X	-	0.53	0.57	0.50	4	536	6	1	3	2	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2ZY6_A	-	0.66	0.78	0.58	7	264	5	3	2	0	2
2ZZM_B	tRNA links to Rfam database...	0.25	0.27	0.25	4	1342	20	3	9	8	11
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	3	2	0	1	1
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.86	0.85	0.88	28	1787	5	0	4	1	5
3AKZ_H	tRNA links to Rfam database...	0.48	0.50	0.48	10	1106	13	4	7	2	10
3AM1_B	-	0.86	0.86	0.86	25	1437	4	0	4	0	4
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3DW4_A	-	-0.03	0.00	0.00	0	136	6	1	3	2	6
3G4S_9	5S_rRNA links to Rfam database...	0.78	0.77	0.80	20	2711	14	2	3	9	6
3GCA_A	-	0.84	0.71	1.00	5	153	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
3HAY_E	-	1.00	1.00	1.00	14	910	7	0	0	7	0
3HJW_D	-	1.00	1.00	1.00	16	593	2	0	0	2	0
3IAB_R	-	1.00	1.00	1.00	12	373	0	0	0	0	0
3ID5_D	-	0.59	0.60	0.60	3	224	5	0	2	3	2
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.69	0.68	0.70	19	1445	9	1	7	1	9
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
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	9	0	5	4	3
3J0L_g	-	-0.01	0.00	0.00	0	173	5	1	2	2	2
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.55	0.64	0.50	7	397	8	5	2	1	4
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_h	-	0.87	0.81	0.93	26	2112	4	1	1	2	6
3J0L_7	-	0.38	0.50	0.31	5	503	12	4	7	1	5
3J0L_2	-	0.34	0.35	0.35	9	2224	23	2	15	6	17
3J16_L	tRNA links to Rfam database...	0.31	0.33	0.30	7	1136	16	3	13	0	14
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J20_1	tRNA links to Rfam database...	0.75	0.75	0.75	15	1092	8	0	5	3	5
3J2C_O	-	0.71	0.68	0.74	28	3949	15	3	7	5	13
3J2C_M	-	0.83	0.85	0.81	82	39824	58	8	11	39	14
3J2L_3	5S_rRNA links to Rfam database...	0.80	0.82	0.78	28	2984	12	1	7	4	6
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1089	22	4	18	0	20
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	27	0	4	23	3
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	31	10	2	19	2
3KTW_C	-	0.96	0.96	0.96	24	1755	9	0	1	8	1
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NDB_M	-	1.00	1.00	1.00	44	3670	4	0	0	4	0
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NMU_E	-	1.00	1.00	1.00	3	213	5	0	0	5	0
3NPB_A	SAM links to Rfam database...	0.85	0.78	0.94	29	2247	6	0	2	4	8
3O58_2	5S_rRNA links to Rfam database...	0.87	0.87	0.87	27	2723	12	0	4	8	4
3O58_3	5_8S_rRNA links to Rfam database...	0.26	0.36	0.19	8	4722	35	16	18	1	14
3OVB_D	-	1.00	1.00	1.00	11	215	1	0	0	1	0
3OVS_D	-	1.00	1.00	1.00	12	204	0	0	0	0	0
3P22_G	-	1.00	1.00	1.00	11	301	0	0	0	0	0
3PDR_A	ykoK links to Rfam database...	0.81	0.80	0.82	40	4791	11	3	6	2	10
3R4F_A	-	1.00	1.00	1.00	22	884	1	0	0	1	0
3R9X_C	-	1.00	1.00	1.00	8	221	2	0	0	2	0
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
3SIU_F	-	1.00	1.00	1.00	8	137	0	0	0	0	0
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3TRZ_Z	-	1.00	1.00	1.00	5	87	1	0	0	1	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3UZL_B	tRNA links to Rfam database...	0.49	0.50	0.50	8	1277	15	0	8	7	8
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.60	0.61	0.61	20	1956	14	4	9	1	13
3ZEX_G	-	0.86	0.84	0.88	38	6464	22	0	5	17	7
3ZEX_H	-	0.26	0.37	0.19	7	3588	30	19	11	0	12
3ZEX_D	5S_rRNA links to Rfam database...	0.90	0.86	0.94	30	2764	6	0	2	4	5
3ZEX_F	-	-0.01	0.00	0.00	0	908	11	2	4	5	4
3ZEX_E	-	0.00	0.00	0.00	0	8255	54	17	32	5	34
3ZEX_C	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	5328	46	11	35	0	29
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	7	0	4	3	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	42	12	16	14	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ATO_G	-	0.72	1.00	0.54	7	207	6	6	0	0	0
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
4FNJ_A	-	0.91	0.83	1.00	10	240	0	0	0	0	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.59	0.57	0.62	16	1822	10	2	8	0	12
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

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Performance of Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	1906
Total TN	231774
Total FP	1075
Total FP CONTRA	263
Total FP INCONS	479
Total FP COMP	333
Total FN	618

Total Scores
MCC	0.734
Average MCC ± 95% Confidence Intervals	0.784 ± 0.049
Sensitivity	0.755
Positive Predictive Value	0.720
Nr of predictions	135

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2K5Z_A	-	1.00	1.00	1.00	11	175	0	0	0	0	0
2K63_A	-	1.00	1.00	1.00	9	159	2	0	0	2	0
2K66_A	-	1.00	1.00	1.00	9	80	0	0	0	0	0
2KD8_A	-	1.00	1.00	1.00	9	99	0	0	0	0	0
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
2KEZ_A	-	1.00	1.00	1.00	8	94	0	0	0	0	0
2KFC_A	-	0.71	0.63	0.83	5	230	1	1	0	0	3
2KGP_A	-	1.00	1.00	1.00	9	112	1	0	0	1	0
2KMJ_A	-	1.00	1.00	1.00	11	157	0	0	0	0	0
2KPV_A	-	1.00	1.00	1.00	13	200	0	0	0	0	0
2KRL_A	-	0.91	0.87	0.95	20	2003	9	1	0	8	3
2KU0_A	-	0.63	0.58	0.70	7	282	3	2	1	0	5
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
2KXM_A	-	1.00	1.00	1.00	8	141	0	0	0	0	0
2KZL_A	-	1.00	1.00	1.00	13	507	5	0	0	5	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	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
2L2K_A	-	1.00	1.00	1.00	17	332	0	0	0	0	0
2L3C_B	-	1.00	1.00	1.00	14	225	0	0	0	0	0
2L3E_A	-	1.00	1.00	1.00	12	228	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	1.00	1.00	1.00	30	955	0	0	0	0	0
2L5Z_A	-	1.00	1.00	1.00	9	102	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	0.94	0.94	0.94	17	339	2	0	1	1	1
2LA5_A	-	0.77	0.71	0.83	5	269	3	0	1	2	2
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.39	0.58	7	516	5	3	2	0	11
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.88	0.90	0.87	26	2410	11	0	4	7	3
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	1.00	1.00	1.00	11	196	1	0	0	1	0
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2RPT_A	-	1.00	1.00	1.00	7	65	0	0	0	0	0
2RRC_A	-	1.00	1.00	1.00	7	68	0	0	0	0	0
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2WW9_E	-	0.00	0.00	0.00	0	172	0	0	0	0	5
2WW9_D	-	0.63	0.40	1.00	4	737	5	0	0	5	6
2WW9_F	-	0.68	0.75	0.67	6	103	4	1	2	1	2
2WWQ_V	tRNA links to Rfam database...	1.00	1.00	1.00	19	1185	4	0	0	4	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	27	0	6	21	3
2XQD_Y	tRNA links to Rfam database...	0.85	0.86	0.86	18	1108	4	0	3	1	3
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.10	0.11	0.12	4	2012	30	2	27	1	31
2Y8W_B	-	1.00	1.00	1.00	6	82	3	0	0	3	0
2Y9C_V	-	0.79	0.83	0.75	15	886	8	0	5	3	3
2YIE_X	-	1.00	1.00	1.00	7	537	4	0	0	4	0
2YIE_Z	-	0.53	0.63	0.45	5	591	6	4	2	0	3
2ZY6_A	-	0.69	0.78	0.64	7	265	5	2	2	1	2
2ZZM_B	tRNA links to Rfam database...	0.80	0.80	0.80	12	1343	13	0	3	10	3
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	3	2	0	1	1
3A2K_C	tRNA links to Rfam database...	0.49	0.55	0.46	12	1082	14	3	11	0	10
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.98	0.97	1.00	32	1787	0	0	0	0	1
3AKZ_H	tRNA links to Rfam database...	0.44	0.50	0.40	10	1102	18	6	9	3	10
3AM1_B	-	0.74	0.76	0.73	22	1436	8	3	5	0	7
3AMU_B	tRNA links to Rfam database...	0.75	0.79	0.71	15	1136	9	0	6	3	4
3DW4_A	-	-0.03	0.00	0.00	0	136	6	1	3	2	6
3G4S_9	5S_rRNA links to Rfam database...	0.45	0.50	0.42	13	2705	24	6	12	6	13
3GCA_A	-	0.76	0.71	0.83	5	152	1	1	0	0	2
3GX2_A	SAM links to Rfam database...	0.93	0.89	0.96	25	1423	2	1	0	1	3
3HAY_E	-	1.00	1.00	1.00	14	910	7	0	0	7	0
3HJW_D	-	1.00	1.00	1.00	16	593	2	0	0	2	0
3IAB_R	-	1.00	1.00	1.00	12	373	4	0	0	4	0
3ID5_D	-	0.66	0.60	0.75	3	225	6	0	1	5	2
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.86	0.79	0.96	22	1449	1	0	1	0	6
3IYQ_A	tmRNA links to Rfam database...	0.28	0.39	0.20	20	22341	95	44	35	16	31
3IZ4_A	tmRNA links to Rfam database...	0.57	0.58	0.57	55	25440	49	18	23	8	40
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	11	0	5	6	3
3J0L_g	-	0.00	0.00	0.00	0	176	1	0	0	1	2
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.53	0.55	0.55	6	400	6	3	2	1	5
3J0L_1	-	0.83	0.77	0.91	10	473	3	0	1	2	3
3J0L_h	-	0.87	0.88	0.88	28	2108	6	0	4	2	4
3J0L_7	-	-0.02	0.00	0.00	0	512	7	1	6	0	10
3J0L_2	-	0.28	0.31	0.28	8	2221	26	2	19	5	18
3J16_L	tRNA links to Rfam database...	0.55	0.57	0.55	12	1137	10	3	7	0	9
3J20_0	tRNA links to Rfam database...	0.53	0.57	0.50	12	1195	13	3	9	1	9
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	5	0	0	5	0
3J2C_O	-	0.96	0.95	0.98	39	3947	7	0	1	6	2
3J2C_M	-	0.57	0.63	0.52	60	39809	77	21	35	21	36
3J2L_3	5S_rRNA links to Rfam database...	0.74	0.76	0.72	26	2984	16	1	9	6	8
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1091	20	4	16	0	20
3JYX_3	5S_rRNA links to Rfam database...	0.33	0.47	0.24	7	2349	24	16	6	2	8
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.58	0.27	7	4730	35	13	6	16	5
3KTW_C	-	0.56	0.60	0.54	15	1752	20	2	11	7	10
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NDB_M	-	0.98	0.98	0.98	43	3670	6	0	1	5	1
3NKB_B	-	0.63	0.68	0.59	13	713	9	0	9	0	6
3NMU_E	-	1.00	1.00	1.00	3	213	3	0	0	3	0
3NPB_A	SAM links to Rfam database...	0.86	0.84	0.89	31	2243	9	1	3	5	6
3O58_2	5S_rRNA links to Rfam database...	0.92	0.94	0.91	29	2722	10	0	3	7	2
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.36	0.29	8	4736	21	7	13	1	14
3OVB_D	-	1.00	1.00	1.00	11	215	1	0	0	1	0
3OVS_D	-	1.00	1.00	1.00	12	204	0	0	0	0	0
3P22_G	-	1.00	1.00	1.00	11	301	1	0	0	1	0
3PDR_A	ykoK links to Rfam database...	0.83	0.86	0.80	43	4786	13	5	6	2	7
3R4F_A	-	0.81	0.82	0.82	18	884	5	2	2	1	4
3R9X_C	-	1.00	1.00	1.00	8	221	2	0	0	2	0
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	5	4	0	9
3SIU_F	-	0.87	0.88	0.88	7	137	1	0	1	0	1
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3TRZ_Z	-	1.00	1.00	1.00	5	87	1	0	0	1	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3U4M_B	-	0.81	0.77	0.85	17	1256	5	0	3	2	5
3UZL_B	tRNA links to Rfam database...	0.90	0.88	0.93	14	1278	8	0	1	7	2
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.98	0.97	1.00	32	1957	1	0	0	1	1
3ZEX_G	-	0.35	0.38	0.34	17	6457	42	9	24	9	28
3ZEX_H	-	0.24	0.37	0.17	7	3583	35	22	13	0	12
3ZEX_D	5S_rRNA links to Rfam database...	0.87	0.86	0.88	30	2762	11	0	4	7	5
3ZEX_F	-	0.00	0.00	0.00	0	910	9	0	4	5	4
3ZEX_E	-	-0.01	0.00	0.00	0	8251	58	20	33	5	34
3ZEX_C	5_8S_rRNA links to Rfam database...	0.35	0.34	0.37	10	5347	23	4	13	6	19
4A1C_3	5S_rRNA links to Rfam database...	0.81	0.81	0.81	30	2726	10	0	7	3	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	33	9	13	11	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.53	0.52	0.56	15	1410	13	3	9	1	14
4ATO_G	-	0.52	0.57	0.50	4	212	4	0	4	0	3
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	1	0	0	1	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	1	0	0	1	4
4FNJ_A	-	0.91	0.83	1.00	10	240	0	0	0	0	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.73	0.71	0.77	17	1180	5	3	2	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.74	0.71	0.77	20	1822	6	1	5	0	8
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

^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 HotKnots - scored higher in this pairwise comparison

1. Total counts & total scores for HotKnots

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

Performance of Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

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