# This file is the result of combining several RDB files, specifically # T0373.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0373.t2k.stride-ebghtl.rdb (weight 1.24869) # T0373.t2k.str2.rdb (weight 1.54758) # T0373.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 T0373.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0373 # 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 T0373.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 1386 # # ============================================ # Comments from T0373.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0373 # 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 T0373.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 1386 # # ============================================ # Comments from T0373.t2k.str2.rdb # ============================================ # TARGET T0373 # 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 T0373.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 1386 # # ============================================ # Comments from T0373.t2k.alpha.rdb # ============================================ # TARGET T0373 # 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 T0373.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 1386 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0672 0.0417 0.8911 2 P 0.0815 0.0372 0.8812 3 T 0.0753 0.1245 0.8002 4 N 0.0476 0.2139 0.7385 5 Q 0.0247 0.5593 0.4160 6 D 0.0126 0.7286 0.2588 7 L 0.0087 0.8326 0.1587 8 Q 0.0077 0.9040 0.0883 9 L 0.0049 0.9436 0.0516 10 A 0.0047 0.9570 0.0383 11 A 0.0047 0.9593 0.0360 12 H 0.0047 0.9597 0.0356 13 L 0.0047 0.9603 0.0350 14 R 0.0047 0.9597 0.0356 15 S 0.0047 0.9587 0.0366 16 Q 0.0047 0.9579 0.0374 17 V 0.0047 0.9576 0.0377 18 T 0.0048 0.9534 0.0418 19 T 0.0048 0.9503 0.0449 20 L 0.0049 0.9450 0.0501 21 T 0.0055 0.9330 0.0615 22 R 0.0062 0.9130 0.0807 23 R 0.0069 0.8984 0.0948 24 L 0.0081 0.8823 0.1096 25 R 0.0066 0.8981 0.0953 26 R 0.0055 0.9070 0.0875 27 E 0.0054 0.9073 0.0872 28 A 0.0071 0.8850 0.1079 29 Q 0.0078 0.8461 0.1461 30 A 0.0098 0.7342 0.2560 31 D 0.0456 0.3361 0.6183 32 P 0.0398 0.0535 0.9067 33 V 0.0726 0.0212 0.9062 34 Q 0.0559 0.0168 0.9274 35 F 0.0077 0.8894 0.1029 36 S 0.0050 0.9330 0.0620 37 Q 0.0049 0.9521 0.0431 38 L 0.0050 0.9591 0.0359 39 V 0.0056 0.9585 0.0359 40 V 0.0056 0.9585 0.0359 41 L 0.0065 0.9569 0.0366 42 G 0.0056 0.9567 0.0377 43 A 0.0054 0.9533 0.0413 44 I 0.0058 0.9347 0.0594 45 D 0.0083 0.8818 0.1099 46 R 0.0117 0.7622 0.2261 47 L 0.0423 0.5005 0.4572 48 G 0.0400 0.1431 0.8169 49 G 0.0422 0.0832 0.8746 50 D 0.0719 0.0531 0.8749 51 V 0.1412 0.0187 0.8402 52 T 0.1216 0.0136 0.8648 53 P 0.0076 0.9152 0.0772 54 S 0.0048 0.9414 0.0539 55 E 0.0050 0.9504 0.0446 56 L 0.0050 0.9536 0.0415 57 A 0.0051 0.9476 0.0474 58 A 0.0054 0.9303 0.0643 59 A 0.0065 0.8886 0.1050 60 E 0.0440 0.5274 0.4286 61 R 0.0335 0.1169 0.8497 62 M 0.0843 0.0505 0.8652 63 R 0.0755 0.0346 0.8899 64 S 0.0295 0.5890 0.3815 65 S 0.0095 0.7431 0.2473 66 N 0.0125 0.8433 0.1442 67 L 0.0059 0.9310 0.0630 68 A 0.0047 0.9549 0.0403 69 A 0.0047 0.9571 0.0382 70 L 0.0047 0.9588 0.0365 71 L 0.0047 0.9586 0.0366 72 R 0.0048 0.9586 0.0366 73 E 0.0048 0.9582 0.0370 74 L 0.0049 0.9563 0.0388 75 E 0.0056 0.9392 0.0552 76 R 0.0063 0.8726 0.1210 77 G 0.0433 0.2726 0.6841 78 G 0.0338 0.0301 0.9362 79 L 0.1562 0.0338 0.8100 80 I 0.7152 0.0152 0.2696 81 V 0.7730 0.0182 0.2088 82 R 0.7532 0.0170 0.2297 83 H 0.6168 0.0107 0.3725 84 A 0.3591 0.0143 0.6265 85 D 0.1680 0.0129 0.8191 86 P 0.0165 0.3314 0.6521 87 Q 0.0208 0.2435 0.7357 88 D 0.0963 0.2619 0.6419 89 G 0.1027 0.1219 0.7754 90 R 0.4324 0.0532 0.5144 91 R 0.7737 0.0161 0.2101 92 T 0.8603 0.0097 0.1300 93 R 0.8999 0.0058 0.0942 94 V 0.8839 0.0065 0.1096 95 S 0.8422 0.0053 0.1525 96 L 0.5513 0.0091 0.4397 97 S 0.1105 0.0128 0.8768 98 S 0.0068 0.8092 0.1840 99 E 0.0082 0.8933 0.0985 100 G 0.0063 0.9236 0.0700 101 R 0.0050 0.9497 0.0453 102 R 0.0048 0.9499 0.0452 103 N 0.0050 0.9431 0.0520 104 L 0.0053 0.9357 0.0590 105 Y 0.0063 0.9103 0.0834 106 G 0.0078 0.8605 0.1317 107 N 0.0101 0.8210 0.1689 108 R 0.0095 0.8547 0.1358 109 A 0.0059 0.8847 0.1094 110 K 0.0062 0.9045 0.0893 111 R 0.0066 0.9097 0.0836 112 E 0.0060 0.9146 0.0794 113 E 0.0057 0.9255 0.0688 114 W 0.0057 0.9273 0.0670 115 L 0.0054 0.9208 0.0738 116 V 0.0053 0.9184 0.0762 117 R 0.0055 0.9122 0.0824 118 A 0.0058 0.9020 0.0923 119 M 0.0072 0.8528 0.1400 120 H 0.0090 0.7509 0.2401 121 A 0.0201 0.4781 0.5018 122 C 0.0219 0.2001 0.7780 123 L 0.0570 0.0275 0.9155 124 D 0.0460 0.0194 0.9346 125 E 0.0051 0.9184 0.0765 126 S 0.0048 0.9420 0.0533 127 E 0.0049 0.9516 0.0435 128 R 0.0047 0.9589 0.0364 129 A 0.0047 0.9553 0.0400 130 L 0.0047 0.9541 0.0412 131 L 0.0048 0.9540 0.0412 132 A 0.0047 0.9570 0.0383 133 A 0.0048 0.9551 0.0401 134 A 0.0048 0.9515 0.0437 135 G 0.0047 0.9561 0.0392 136 P 0.0047 0.9548 0.0405 137 L 0.0047 0.9544 0.0409 138 L 0.0047 0.9519 0.0434 139 T 0.0049 0.9443 0.0508 140 R 0.0052 0.8971 0.0977 141 L 0.0086 0.8158 0.1756 142 A 0.0345 0.6521 0.3134 143 Q 0.0163 0.5154 0.4683 144 F 0.0227 0.3994 0.5779 145 E 0.0502 0.2099 0.7399 146 E 0.0487 0.0759 0.8754 147 P 0.0428 0.0434 0.9138