CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAshapes		RNAsubopt
MCC	0.759	>	0.738
Average MCC ± 95% Confidence Intervals	0.791 ± 0.053	>	0.770 ± 0.057
Sensitivity	0.770	>	0.757
Positive Predictive Value	0.755	>	0.726
Total TP	1567	>	1542
Total TN	149960	>	149912
Total FP	782	<	846
Total FP CONTRA	148	<	185
Total FP INCONS	360	<	396
Total FP COMP	274	>	265
Total FN	469	<	494
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RNAshapes and RNAsubopt. 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 RNAshapes and RNAsubopt).
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 RNAshapes and RNAsubopt).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAshapes and RNAsubopt. 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 RNAshapes and RNAsubopt).

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Performance of RNAshapes - scored higher in this pairwise comparison

1. Total counts & total scores for RNAshapes

Total Base Pair Counts
Total TP	1567
Total TN	149960
Total FP	782
Total FP CONTRA	148
Total FP INCONS	360
Total FP COMP	274
Total FN	469

Total Scores
MCC	0.759
Average MCC ± 95% Confidence Intervals	0.791 ± 0.053
Sensitivity	0.770
Positive Predictive Value	0.755
Nr of predictions	118

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2. Individual counts for RNAshapes [ 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...	0.97	0.94	1.00	15	356	0	0	0	0	1
2KXM_A	-	0.93	0.88	1.00	7	142	0	0	0	0	1
2KZL_A	-	1.00	1.00	1.00	13	507	1	0	0	1	0
2L1F_A	Gammaretro_CES links to Rfam database...	0.89	0.87	0.91	20	741	2	0	2	0	3
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	768	0	0	0	0	1
2L2K_A	-	0.97	0.94	1.00	16	333	0	0	0	0	1
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...	0.98	0.97	1.00	29	956	0	0	0	0	1
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	6	0	0	6	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	-	0.83	0.71	1.00	5	70	0	0	0	0	2
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	13	0	0	13	0
2WW9_D	-	0.11	0.10	0.14	1	734	11	2	4	5	9
2WW9_E	-	0.89	0.80	1.00	4	168	0	0	0	0	1
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	24	0	6	18	3
2XQD_Y	tRNA links to Rfam database...	0.70	0.67	0.74	14	1110	6	0	5	1	7
2XXA_G	Bacteria_small_SRP links to Rfam database...	1.00	1.00	1.00	35	2010	1	0	0	1	0
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	-	0.33	0.43	0.27	3	533	11	3	5	3	4
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
2ZY6_A	-	0.69	0.78	0.64	7	265	5	2	2	1	2
2ZZM_B	tRNA links to Rfam database...	0.05	0.07	0.06	1	1340	25	4	13	8	14
2ZZN_D	tRNA links to Rfam database...	0.77	0.77	0.77	17	962	5	1	4	0	5
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...	0.84	0.80	0.89	24	1473	3	0	3	0	6
3ADB_C	-	0.71	0.70	0.74	23	1788	8	0	8	0	10
3AKZ_H	tRNA links to Rfam database...	0.78	0.80	0.76	16	1106	7	2	3	2	4
3AM1_B	-	0.71	0.72	0.70	21	1436	9	3	6	0	8
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	137	3	0	3	0	6
3G4S_9	5S_rRNA links to Rfam database...	0.58	0.58	0.60	15	2711	19	2	8	9	11
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.91	0.89	0.93	25	1422	3	1	1	1	3
3HAY_E	-	1.00	1.00	1.00	14	910	5	0	0	5	0
3HJW_D	-	1.00	1.00	1.00	16	593	0	0	0	0	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...	0.83	0.79	0.88	22	1447	3	1	2	0	6
3IYQ_A	tmRNA links to Rfam database...	0.19	0.27	0.14	14	22340	95	43	43	9	37
3IZ4_A	tmRNA links to Rfam database...	0.57	0.58	0.56	55	25437	50	16	28	6	40
3IZF_C	5S_rRNA links to Rfam database...	0.76	0.77	0.75	27	2604	14	0	9	5	8
3J0L_h	-	0.87	0.81	0.93	26	2112	4	1	1	2	6
3J0L_g	-	-0.01	0.00	0.00	0	174	4	0	2	2	2
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3J0L_2	-	0.46	0.46	0.48	12	2225	20	1	12	7	14
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_7	-	-0.02	0.00	0.00	0	507	12	2	10	0	10
3J16_L	tRNA links to Rfam database...	0.59	0.57	0.63	12	1140	7	0	7	0	9
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1092	20	1	18	1	20
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	26	0	4	22	3
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	35	10	2	23	2
3KTW_C	-	0.57	0.60	0.56	15	1753	19	2	10	7	10
3LA5_A	Purine links to Rfam database...	0.89	0.80	1.00	20	934	0	0	0	0	5
3NDB_M	-	0.98	0.98	0.98	43	3670	5	0	1	4	1
3NKB_B	-	0.75	0.74	0.78	14	717	6	0	4	2	5
3NMU_E	-	1.00	1.00	1.00	3	213	5	0	0	5	0
3NPB_A	SAM links to Rfam database...	0.84	0.76	0.93	28	2248	5	1	1	3	9
3O58_2	5S_rRNA links to Rfam database...	0.73	0.74	0.72	23	2722	18	0	9	9	8
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
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...	0.80	0.80	0.80	40	4790	12	3	7	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...	0.43	0.50	0.38	8	1272	17	4	9	4	8
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	11	16	14	15
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	7	0	4	3	6
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
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10

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Performance of RNAsubopt - scored lower in this pairwise comparison

1. Total counts & total scores for RNAsubopt

Total Base Pair Counts
Total TP	1542
Total TN	149912
Total FP	846
Total FP CONTRA	185
Total FP INCONS	396
Total FP COMP	265
Total FN	494

Total Scores
MCC	0.738
Average MCC ± 95% Confidence Intervals	0.770 ± 0.057
Sensitivity	0.757
Positive Predictive Value	0.726
Nr of predictions	118

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2K5Z_A	-	0.95	0.91	1.00	10	176	0	0	0	0	1
2K63_A	-	0.94	0.89	1.00	8	160	0	0	0	0	1
2K66_A	-	1.00	1.00	1.00	9	80	0	0	0	0	0
2KD8_A	-	0.87	0.78	1.00	7	101	0	0	0	0	2
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...	0.88	0.89	0.89	16	449	3	0	2	1	2
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	0	0	0	0	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	-	0.62	0.61	0.64	14	2002	15	5	3	7	9
2KU0_A	-	0.96	0.92	1.00	11	281	0	0	0	0	1
2KUR_A	K10_TLS links to Rfam database...	0.89	0.89	0.89	17	448	2	0	2	0	2
2KUU_A	K10_TLS links to Rfam database...	0.88	0.89	0.89	16	429	3	0	2	1	2
2KUV_A	K10_TLS links to Rfam database...	0.89	0.89	0.89	17	420	2	0	2	0	2
2KUW_A	K10_TLS links to Rfam database...	0.94	0.94	0.94	17	452	2	0	1	1	1
2KX8_A	7SK links to Rfam database...	0.97	0.94	1.00	15	356	0	0	0	0	1
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_A	Gammaretro_CES links to Rfam database...	0.95	0.91	1.00	21	742	0	0	0	0	2
2L1F_B	Gammaretro_CES links to Rfam database...	0.96	0.92	1.00	22	769	0	0	0	0	2
2L2K_A	-	1.00	1.00	1.00	17	332	0	0	0	0	0
2L3C_B	-	0.96	0.93	1.00	13	226	0	0	0	0	1
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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
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	-	0.85	0.86	0.83	25	2410	14	0	5	9	4
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	13	0	0	13	0
2WW9_D	-	0.09	0.10	0.11	1	732	13	2	6	5	9
2WW9_E	-	-0.03	0.00	0.00	0	168	5	0	4	1	5
2WW9_F	-	0.52	0.63	0.50	5	102	5	1	4	0	3
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...	0.83	0.81	0.85	17	1109	4	0	3	1	4
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.49	0.49	0.52	17	2012	17	1	15	1	18
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	-	1.00	1.00	1.00	7	537	4	0	0	4	0
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...	0.29	0.33	0.26	5	1339	22	5	9	8	10
2ZZN_D	tRNA links to Rfam database...	0.52	0.55	0.52	12	961	11	3	8	0	10
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	-	0.98	0.97	1.00	32	1787	0	0	0	0	1
3AKZ_H	tRNA links to Rfam database...	0.43	0.45	0.43	9	1106	14	3	9	2	11
3AM1_B	-	1.00	1.00	1.00	29	1437	0	0	0	0	0
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...	0.41	0.46	0.38	12	2704	25	7	13	5	14
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.53	0.54	0.54	15	1421	14	4	9	1	13
3HAY_E	-	1.00	1.00	1.00	14	910	4	0	0	4	0
3HJW_D	-	0.97	0.94	1.00	15	594	2	0	0	2	1
3IAB_R	-	1.00	1.00	1.00	12	373	0	0	0	0	0
3ID5_D	-	0.54	0.60	0.50	3	223	5	1	2	2	2
3IVN_B	Purine links to Rfam database...	0.88	0.78	1.00	18	885	0	0	0	0	5
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...	0.28	0.39	0.20	20	22342	96	41	37	18	31
3IZ4_A	tmRNA links to Rfam database...	0.56	0.60	0.53	57	25429	54	26	24	4	38
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	9	0	5	4	3
3J0L_h	-	0.87	0.81	0.93	26	2112	4	1	1	2	6
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	-	0.35	0.36	0.36	4	400	8	3	4	1	7
3J0L_2	-	0.28	0.31	0.28	8	2221	25	2	19	4	18
3J0L_1	-	0.83	0.77	0.91	10	473	4	0	1	3	3
3J0L_7	-	-0.02	0.00	0.00	0	507	12	2	10	0	10
3J16_L	tRNA links to Rfam database...	0.49	0.52	0.48	11	1136	12	3	9	0	10
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1090	21	4	17	0	20
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	26	0	4	22	3
3JYX_4	5_8S_rRNA links to Rfam database...	0.34	0.58	0.21	7	4722	38	20	7	11	5
3KTW_C	-	1.00	1.00	1.00	25	1755	8	0	0	8	0
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NDB_M	-	0.93	0.93	0.93	41	3670	9	0	3	6	3
3NKB_B	-	0.66	0.68	0.65	13	715	7	0	7	0	6
3NMU_E	-	1.00	1.00	1.00	3	213	5	0	0	5	0
3NPB_A	SAM links to Rfam database...	0.84	0.78	0.91	29	2246	8	0	3	5	8
3O58_2	5S_rRNA links to Rfam database...	0.87	0.90	0.85	28	2721	13	0	5	8	3
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	35	6	15	14	11
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...	0.90	0.90	0.90	45	4790	7	2	3	2	5
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...	0.73	0.72	0.75	21	1505	7	4	3	0	8
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4481	43	13	17	13	15
4A1C_3	5S_rRNA links to Rfam database...	0.85	0.84	0.86	31	2727	8	0	5	3	6
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.62	0.62	0.64	18	1409	11	4	6	1	11
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	7	0	7	0	10

^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 RNAshapes - scored higher in this pairwise comparison

1. Total counts & total scores for RNAshapes

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

Performance of RNAsubopt - scored lower in this pairwise comparison

1. Total counts & total scores for RNAsubopt

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