# This file is the result of combining several RDB files, specifically # T0347.t06.dssp-ebghstl.rdb (weight 1.53986) # T0347.t06.stride-ebghtl.rdb (weight 1.24869) # T0347.t06.str2.rdb (weight 1.54758) # T0347.t06.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 T0347.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0347 # Using neural net t06-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 T0347.t06-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 13.3407 # # ============================================ # Comments from T0347.t06.stride-ebghtl.rdb # ============================================ # TARGET T0347 # Using neural net t06-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 T0347.t06-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 13.3407 # # ============================================ # Comments from T0347.t06.str2.rdb # ============================================ # TARGET T0347 # Using neural net t06-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 T0347.t06-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 13.3407 # # ============================================ # Comments from T0347.t06.alpha.rdb # ============================================ # TARGET T0347 # Using neural net t06-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 T0347.t06-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 13.3407 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.0430 0.0211 0.9359 2 K 0.0402 0.2399 0.7200 3 D 0.0184 0.6874 0.2942 4 E 0.0158 0.8029 0.1813 5 F 0.0091 0.9064 0.0845 6 W 0.0070 0.9257 0.0673 7 S 0.0080 0.9283 0.0637 8 V 0.0096 0.9255 0.0649 9 M 0.0220 0.8682 0.1098 10 D 0.0145 0.7547 0.2308 11 H 0.0155 0.4658 0.5187 12 R 0.0533 0.1383 0.8084 13 N 0.0550 0.0358 0.9092 14 L 0.3264 0.0182 0.6555 15 I 0.6872 0.0093 0.3035 16 Y 0.7442 0.0081 0.2477 17 P 0.6272 0.0338 0.3390 18 F 0.5375 0.0372 0.4253 19 D 0.1952 0.0238 0.7810 20 A 0.0173 0.1672 0.8155 21 Q 0.0499 0.0545 0.8956 22 G 0.0618 0.0476 0.8906 23 L 0.1733 0.0194 0.8073 24 R 0.4907 0.0156 0.4938 25 R 0.2328 0.0260 0.7412 26 Q 0.1673 0.0393 0.7934 27 S 0.0330 0.5776 0.3894 28 G 0.0182 0.5428 0.4390 29 D 0.0272 0.5542 0.4187 30 I 0.0794 0.1545 0.7660 31 P 0.0724 0.1909 0.7367 32 K 0.0387 0.5293 0.4320 33 N 0.0535 0.4656 0.4810 34 I 0.0509 0.6239 0.3252 35 H 0.0331 0.5463 0.4206 36 D 0.0476 0.4411 0.5112 37 L 0.0501 0.4541 0.4958 38 E 0.0498 0.2808 0.6695 39 D 0.0499 0.1739 0.7762 40 D 0.0907 0.0489 0.8604 41 P 0.0107 0.6076 0.3817 42 F 0.0147 0.7418 0.2435 43 R 0.0156 0.8450 0.1394 44 S 0.0193 0.8955 0.0853 45 L 0.0118 0.9320 0.0562 46 A 0.0119 0.9392 0.0489 47 G 0.0120 0.9434 0.0446 48 A 0.0119 0.9458 0.0423 49 L 0.0210 0.9303 0.0487 50 R 0.0306 0.8947 0.0747 51 M 0.0265 0.8401 0.1334 52 A 0.0425 0.4868 0.4707 53 G 0.0337 0.0837 0.8826 54 G 0.0737 0.1147 0.8116 55 Y 0.2103 0.1442 0.6455 56 A 0.2205 0.1502 0.6293 57 K 0.2075 0.1014 0.6911 58 V 0.2083 0.0705 0.7212 59 I 0.2722 0.0540 0.6738 60 I 0.2186 0.0346 0.7468 61 P 0.1710 0.0815 0.7475 62 F 0.0991 0.4077 0.4932 63 S 0.0666 0.5712 0.3622 64 E 0.0740 0.6391 0.2869 65 F 0.0900 0.6168 0.2932 66 G 0.0808 0.6637 0.2555 67 W 0.0256 0.8547 0.1197 68 A 0.0101 0.9213 0.0686 69 D 0.0074 0.9411 0.0516 70 F 0.0069 0.9378 0.0553 71 L 0.0064 0.9227 0.0709 72 R 0.0076 0.8764 0.1159 73 R 0.0096 0.7836 0.2068 74 R 0.0176 0.5981 0.3843 75 I 0.0537 0.3123 0.6340 76 D 0.0589 0.1722 0.7689 77 R 0.0180 0.6465 0.3355 78 D 0.0163 0.6609 0.3229 79 L 0.0172 0.7115 0.2713 80 L 0.0458 0.4666 0.4877 81 S 0.0423 0.3353 0.6224 82 D 0.0226 0.3663 0.6111 83 S 0.0350 0.3052 0.6599 84 F 0.0227 0.5666 0.4107 85 D 0.0093 0.8747 0.1161 86 D 0.0053 0.9217 0.0730 87 A 0.0050 0.9353 0.0597 88 L 0.0048 0.9469 0.0483 89 A 0.0047 0.9538 0.0415 90 E 0.0048 0.9477 0.0475 91 A 0.0049 0.9461 0.0490 92 M 0.0048 0.9453 0.0499 93 K 0.0049 0.9254 0.0697 94 L 0.0058 0.8580 0.1362 95 A 0.0112 0.7273 0.2616 96 K 0.0219 0.5149 0.4632 97 S 0.0519 0.2900 0.6581 98 R 0.0078 0.5935 0.3988 99 E 0.0117 0.5723 0.4160 100 A 0.0252 0.6599 0.3149 101 R 0.0285 0.4967 0.4747 102 H 0.0475 0.3233 0.6292 103 L 0.1096 0.0591 0.8313 104 P 0.0814 0.1357 0.7829 105 G 0.1183 0.1359 0.7458 106 W 0.1846 0.1449 0.6705 107 C 0.1778 0.1154 0.7068 108 G 0.1031 0.0686 0.8283 109 V 0.0977 0.0572 0.8451 110 E 0.0779 0.0566 0.8655 111 E 0.0443 0.0422 0.9134