# This file is the result of combining several RDB files, specifically # T0212.t04.dssp-ebghstl.rdb (weight 1.53986) # T0212.t04.stride-ebghtl.rdb (weight 1.24869) # T0212.t04.str2.rdb (weight 1.54758) # T0212.t04.alpha.rdb (weight 0.659012) # These files were combined by translating their predictions into EHL # predictions with tables generated by compare-real, and then combining # those predictions with weights proportional to their mutual information # with the EHL alphabet. The comments from the individual files follow. # # Comments from T0212.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0212 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0212.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 9.68939 # # ============================================ # Comments from T0212.t04.stride-ebghtl.rdb # ============================================ # TARGET T0212 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0212.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 9.68939 # # ============================================ # Comments from T0212.t04.str2.rdb # ============================================ # TARGET T0212 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0212.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 9.68939 # # ============================================ # Comments from T0212.t04.alpha.rdb # ============================================ # TARGET T0212 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0212.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 9.68939 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1440 0.0499 0.8062 2 S 0.2534 0.0755 0.6712 3 A 0.3069 0.0861 0.6070 4 L 0.3144 0.0964 0.5892 5 D 0.2258 0.0845 0.6897 6 N 0.1495 0.0703 0.7802 7 S 0.3333 0.0257 0.6410 8 I 0.7499 0.0048 0.2453 9 R 0.8904 0.0038 0.1059 10 V 0.9138 0.0036 0.0826 11 E 0.9122 0.0037 0.0841 12 V 0.8866 0.0041 0.1093 13 K 0.7362 0.0105 0.2533 14 T 0.5929 0.0451 0.3619 15 E 0.4313 0.1257 0.4430 16 Y 0.3772 0.1840 0.4388 17 I 0.2797 0.2235 0.4968 18 E 0.2102 0.2998 0.4900 19 Q 0.1730 0.3355 0.4914 20 Q 0.1506 0.2143 0.6351 21 S 0.1228 0.1135 0.7637 22 S 0.0828 0.0305 0.8867 23 P 0.0440 0.1342 0.8218 24 E 0.0386 0.1860 0.7753 25 D 0.0608 0.1951 0.7441 26 E 0.1240 0.1235 0.7525 27 K 0.4814 0.0507 0.4679 28 Y 0.8461 0.0097 0.1443 29 L 0.8824 0.0088 0.1088 30 F 0.9107 0.0058 0.0836 31 S 0.9071 0.0083 0.0845 32 Y 0.9062 0.0065 0.0873 33 T 0.9248 0.0039 0.0713 34 I 0.9241 0.0037 0.0721 35 T 0.9267 0.0040 0.0693 36 I 0.9215 0.0041 0.0745 37 I 0.8493 0.0210 0.1298 38 N 0.6573 0.0121 0.3306 39 L 0.2033 0.0492 0.7474 40 G 0.0880 0.0429 0.8691 41 E 0.1425 0.1199 0.7376 42 Q 0.2954 0.1371 0.5675 43 A 0.5124 0.1205 0.3671 44 A 0.7194 0.0695 0.2111 45 K 0.7954 0.0619 0.1426 46 L 0.7647 0.0717 0.1636 47 E 0.7059 0.0819 0.2122 48 T 0.6631 0.0541 0.2828 49 R 0.6890 0.0276 0.2834 50 H 0.8389 0.0098 0.1512 51 W 0.9042 0.0049 0.0910 52 I 0.9213 0.0048 0.0740 53 I 0.9241 0.0039 0.0720 54 T 0.8788 0.0062 0.1150 55 D 0.4505 0.0187 0.5307 56 A 0.0588 0.1133 0.8279 57 N 0.0523 0.0266 0.9211 58 G 0.0758 0.0297 0.8945 59 K 0.3441 0.0176 0.6384 60 T 0.8086 0.0099 0.1815 61 S 0.7795 0.0209 0.1996 62 E 0.8678 0.0105 0.1217 63 V 0.8833 0.0073 0.1093 64 Q 0.7478 0.0296 0.2225 65 G 0.5727 0.0201 0.4072 66 A 0.3946 0.0505 0.5548 67 G 0.5002 0.0383 0.4615 68 V 0.6084 0.0419 0.3497 69 V 0.5187 0.0523 0.4290 70 G 0.3782 0.0474 0.5744 71 E 0.3548 0.0478 0.5974 72 T 0.2483 0.0326 0.7192 73 P 0.2051 0.0348 0.7601 74 T 0.3144 0.0354 0.6501 75 I 0.1938 0.0124 0.7938 76 P 0.0848 0.0154 0.8998 77 P 0.0348 0.0889 0.8763 78 N 0.0340 0.0635 0.9025 79 T 0.1615 0.0513 0.7872 80 A 0.4771 0.0323 0.4906 81 Y 0.7985 0.0183 0.1832 82 Q 0.8507 0.0127 0.1365 83 Y 0.8128 0.0127 0.1745 84 T 0.7012 0.0226 0.2761 85 S 0.4808 0.0347 0.4845 86 G 0.4341 0.0664 0.4995 87 T 0.5299 0.0678 0.4023 88 V 0.5983 0.0586 0.3431 89 L 0.5014 0.0393 0.4592 90 D 0.3620 0.0321 0.6059 91 T 0.1272 0.0204 0.8524 92 P 0.1175 0.0705 0.8120 93 F 0.1892 0.0867 0.7241 94 G 0.3685 0.0712 0.5602 95 I 0.5544 0.0589 0.3867 96 M 0.7200 0.0358 0.2442 97 Y 0.6914 0.0454 0.2632 98 G 0.6797 0.0205 0.2998 99 T 0.7585 0.0271 0.2144 100 Y 0.8263 0.0201 0.1536 101 G 0.8422 0.0134 0.1445 102 M 0.8869 0.0078 0.1054 103 V 0.8639 0.0102 0.1259 104 S 0.5958 0.0137 0.3905 105 E 0.1472 0.0871 0.7656 106 S 0.0646 0.0264 0.9090 107 G 0.0867 0.0332 0.8801 108 E 0.3660 0.0129 0.6211 109 H 0.8876 0.0039 0.1085 110 F 0.8838 0.0051 0.1111 111 N 0.8953 0.0038 0.1009 112 A 0.8703 0.0041 0.1256 113 I 0.8571 0.0044 0.1385 114 I 0.6660 0.0072 0.3268 115 K 0.3427 0.0213 0.6360 116 P 0.3370 0.0536 0.6094 117 F 0.4947 0.1050 0.4003 118 R 0.6318 0.1025 0.2657 119 L 0.6291 0.0579 0.3130 120 A 0.5126 0.0500 0.4373 121 T 0.1934 0.0272 0.7794 122 P 0.0660 0.1195 0.8145 123 G 0.0624 0.1380 0.7997 124 L 0.1395 0.1635 0.6970 125 L 0.1394 0.0687 0.7919 126 H 0.0805 0.0410 0.8785