# This file is the result of combining several RDB files, specifically # T0262.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0262.t2k.stride-ebghtl.rdb (weight 1.24869) # T0262.t2k.str2.rdb (weight 1.54758) # T0262.t2k.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 T0262.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0262 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0262.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 51 # # ============================================ # Comments from T0262.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0262 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0262.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 51 # # ============================================ # Comments from T0262.t2k.str2.rdb # ============================================ # TARGET T0262 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0262.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 51 # # ============================================ # Comments from T0262.t2k.alpha.rdb # ============================================ # TARGET T0262 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0262.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 51 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.0278 0.3107 0.6615 2 S 0.0470 0.5388 0.4143 3 K 0.0242 0.7991 0.1768 4 T 0.0186 0.8878 0.0936 5 L 0.0174 0.9082 0.0744 6 A 0.0231 0.9026 0.0743 7 G 0.0242 0.8997 0.0761 8 I 0.0210 0.8920 0.0870 9 L 0.0195 0.8351 0.1455 10 R 0.0236 0.6209 0.3555 11 H 0.0412 0.4038 0.5550 12 H 0.0385 0.2032 0.7582 13 P 0.0134 0.6728 0.3138 14 G 0.0128 0.7114 0.2758 15 R 0.0215 0.7573 0.2211 16 Y 0.0612 0.3468 0.5920 17 G 0.0750 0.0587 0.8663 18 V 0.2433 0.0168 0.7398 19 R 0.4448 0.0113 0.5439 20 L 0.5421 0.0143 0.4437 21 T 0.1082 0.0225 0.8693 22 R 0.0186 0.1252 0.8562 23 E 0.0551 0.0303 0.9145 24 G 0.0984 0.0434 0.8582 25 W 0.4171 0.0229 0.5600 26 A 0.6865 0.0140 0.2995 27 R 0.4897 0.0250 0.4853 28 V 0.0090 0.9198 0.0712 29 S 0.0048 0.9489 0.0463 30 E 0.0050 0.9536 0.0414 31 V 0.0048 0.9500 0.0452 32 V 0.0055 0.9274 0.0671 33 E 0.0066 0.8805 0.1129 34 G 0.0069 0.8659 0.1272 35 L 0.0164 0.8140 0.1696 36 R 0.0149 0.7058 0.2793 37 K 0.0198 0.6628 0.3174 38 A 0.0270 0.4042 0.5689 39 G 0.0331 0.1578 0.8092 40 W 0.0776 0.1206 0.8017 41 S 0.0536 0.2258 0.7206 42 W 0.0898 0.1590 0.7512 43 V 0.1887 0.0429 0.7684 44 E 0.1284 0.0362 0.8354 45 E 0.0053 0.9391 0.0557 46 W 0.0047 0.9497 0.0455 47 H 0.0048 0.9524 0.0428 48 I 0.0060 0.9538 0.0402 49 V 0.0078 0.9507 0.0415 50 G 0.0083 0.9447 0.0470 51 V 0.0083 0.9346 0.0571 52 A 0.0156 0.8940 0.0904 53 L 0.0188 0.7678 0.2134 54 H 0.0321 0.4009 0.5670 55 D 0.0625 0.0661 0.8714 56 P 0.0246 0.1672 0.8083 57 K 0.0707 0.1675 0.7617 58 G 0.1353 0.1438 0.7209 59 R 0.4752 0.0535 0.4713 60 Y 0.8135 0.0134 0.1732 61 E 0.8657 0.0067 0.1276 62 L 0.8002 0.0111 0.1887 63 R 0.4805 0.0305 0.4891 64 N 0.0919 0.0640 0.8441 65 G 0.1047 0.0743 0.8210 66 E 0.7061 0.0263 0.2676 67 I 0.8211 0.0212 0.1577 68 R 0.8375 0.0271 0.1354 69 A 0.7629 0.0562 0.1809 70 R 0.6218 0.0776 0.3006 71 Y 0.4825 0.0700 0.4475 72 G 0.3441 0.0551 0.6008 73 H 0.3697 0.0388 0.5914 74 S 0.3857 0.0463 0.5680 75 I 0.3991 0.0558 0.5451 76 P 0.4087 0.0538 0.5375 77 V 0.3182 0.0515 0.6303 78 N 0.3188 0.0483 0.6329 79 V 0.2274 0.0857 0.6870 80 E 0.1947 0.0911 0.7142 81 P 0.1517 0.0867 0.7616 82 L 0.1057 0.1076 0.7867 83 P 0.0700 0.2266 0.7034 84 G 0.0672 0.2068 0.7260 85 E 0.0977 0.0917 0.8106 86 P 0.0853 0.0476 0.8671 87 P 0.0910 0.0875 0.8215 88 P 0.1768 0.1532 0.6700 89 I 0.6557 0.1338 0.2105 90 L 0.7756 0.0946 0.1298 91 Y 0.7666 0.0769 0.1565 92 H 0.5455 0.1083 0.3462 93 G 0.1927 0.1039 0.7034 94 T 0.1110 0.1282 0.7608 95 T 0.0604 0.3163 0.6233 96 E 0.0234 0.7044 0.2722 97 E 0.0195 0.7381 0.2424 98 A 0.0202 0.7382 0.2416 99 L 0.0129 0.8647 0.1224 100 P 0.0054 0.9310 0.0636 101 L 0.0056 0.9442 0.0501 102 I 0.0053 0.9478 0.0469 103 M 0.0054 0.9416 0.0530 104 E 0.0058 0.9080 0.0861 105 R 0.0408 0.5549 0.4043 106 G 0.0387 0.1253 0.8360 107 I 0.0851 0.0760 0.8389 108 M 0.1071 0.0812 0.8117 109 R 0.0974 0.3105 0.5921 110 G 0.0829 0.3239 0.5932 111 R 0.1576 0.2245 0.6180 112 R 0.3061 0.0622 0.6317 113 L 0.4201 0.0431 0.5368 114 K 0.8038 0.0197 0.1766 115 V 0.7960 0.0201 0.1839 116 H 0.7708 0.0209 0.2084 117 L 0.6197 0.0331 0.3472 118 T 0.3398 0.0254 0.6348 119 S 0.1252 0.1039 0.7709 120 S 0.1180 0.0661 0.8159 121 L 0.0126 0.8114 0.1761 122 E 0.0098 0.8632 0.1270 123 D 0.0104 0.8528 0.1367 124 A 0.0193 0.7703 0.2104 125 V 0.0369 0.5391 0.4240 126 S 0.0181 0.1306 0.8513