# This file is the result of combining several RDB files, specifically # T0617.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0617.t2k.stride-ebghtl.rdb (weight 1.24869) # T0617.t2k.str2.rdb (weight 1.54758) # T0617.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 T0617.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0617 # 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 T0617.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 4561 # # ============================================ # Comments from T0617.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0617 # 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 T0617.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 4561 # # ============================================ # Comments from T0617.t2k.str2.rdb # ============================================ # TARGET T0617 # 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 T0617.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 4561 # # ============================================ # Comments from T0617.t2k.alpha.rdb # ============================================ # TARGET T0617 # 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 T0617.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 4561 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0744 0.1479 0.7777 2 N 0.0665 0.2105 0.7229 3 A 0.0562 0.2224 0.7214 4 M 0.0630 0.2160 0.7210 5 Q 0.0531 0.2561 0.6908 6 K 0.0666 0.2410 0.6924 7 I 0.0406 0.4179 0.5416 8 N 0.0406 0.4546 0.5047 9 I 0.0261 0.6160 0.3579 10 D 0.0204 0.6793 0.3003 11 R 0.0106 0.7241 0.2653 12 H 0.0095 0.7593 0.2312 13 A 0.0098 0.8617 0.1285 14 T 0.0049 0.9352 0.0599 15 A 0.0047 0.9528 0.0425 16 Q 0.0047 0.9588 0.0366 17 I 0.0047 0.9601 0.0352 18 N 0.0047 0.9601 0.0352 19 M 0.0047 0.9596 0.0357 20 L 0.0047 0.9590 0.0363 21 A 0.0047 0.9580 0.0373 22 N 0.0047 0.9569 0.0383 23 K 0.0049 0.9516 0.0435 24 L 0.0049 0.9486 0.0466 25 M 0.0050 0.9415 0.0536 26 L 0.0055 0.9312 0.0633 27 K 0.0064 0.9084 0.0852 28 S 0.0067 0.8869 0.1064 29 S 0.0085 0.8724 0.1191 30 T 0.0069 0.9029 0.0902 31 A 0.0054 0.9196 0.0749 32 Y 0.0053 0.9246 0.0701 33 T 0.0063 0.9097 0.0840 34 Q 0.0073 0.8782 0.1145 35 K 0.0085 0.7697 0.2217 36 F 0.0458 0.3617 0.5925 37 G 0.0412 0.0490 0.9098 38 I 0.0751 0.0222 0.9027 39 G 0.0582 0.0171 0.9247 40 M 0.0093 0.8713 0.1193 41 T 0.0052 0.9256 0.0691 42 E 0.0053 0.9503 0.0444 43 W 0.0062 0.9571 0.0367 44 R 0.0084 0.9559 0.0357 45 I 0.0084 0.9561 0.0356 46 I 0.0087 0.9554 0.0360 47 S 0.0059 0.9567 0.0374 48 V 0.0063 0.9514 0.0424 49 L 0.0064 0.9332 0.0604 50 S 0.0078 0.8917 0.1005 51 S 0.0124 0.7793 0.2083 52 A 0.0572 0.3183 0.6244 53 S 0.0328 0.0941 0.8731 54 D 0.0429 0.0495 0.9076 55 C 0.1519 0.0168 0.8314 56 S 0.1518 0.0131 0.8351 57 V 0.0098 0.9042 0.0860 58 Q 0.0048 0.9418 0.0534 59 K 0.0051 0.9503 0.0446 60 I 0.0052 0.9525 0.0423 61 S 0.0051 0.9495 0.0454 62 D 0.0055 0.9342 0.0603 63 I 0.0065 0.8912 0.1023 64 L 0.0463 0.5158 0.4379 65 G 0.0337 0.0992 0.8671 66 L 0.0794 0.0446 0.8761 67 D 0.0698 0.0275 0.9027 68 K 0.0234 0.6652 0.3114 69 A 0.0085 0.7993 0.1922 70 A 0.0098 0.8759 0.1144 71 V 0.0064 0.9282 0.0654 72 S 0.0050 0.9518 0.0433 73 R 0.0047 0.9568 0.0385 74 T 0.0047 0.9588 0.0365 75 V 0.0047 0.9593 0.0360 76 K 0.0048 0.9593 0.0359 77 K 0.0048 0.9589 0.0363 78 L 0.0049 0.9570 0.0382 79 E 0.0053 0.9398 0.0550 80 E 0.0055 0.8668 0.1276 81 K 0.0442 0.2468 0.7090 82 K 0.0322 0.0258 0.9420 83 Y 0.1535 0.0312 0.8153 84 I 0.7215 0.0112 0.2673 85 E 0.7884 0.0159 0.1957 86 V 0.7728 0.0154 0.2117 87 N 0.6123 0.0110 0.3768 88 G 0.3003 0.0136 0.6861 89 H 0.1130 0.0123 0.8747 90 S 0.0138 0.4134 0.5728 91 E 0.0195 0.3447 0.6358 92 D 0.0882 0.3900 0.5218 93 K 0.1238 0.2234 0.6528 94 R 0.4247 0.1199 0.4554 95 T 0.7151 0.0465 0.2385 96 Y 0.8063 0.0238 0.1700 97 A 0.8704 0.0135 0.1161 98 I 0.8596 0.0122 0.1283 99 N 0.8019 0.0098 0.1883 100 L 0.5256 0.0125 0.4619 101 T 0.1112 0.0175 0.8712 102 E 0.0083 0.7890 0.2027 103 M 0.0107 0.8659 0.1234 104 G 0.0067 0.9168 0.0765 105 Q 0.0051 0.9452 0.0497 106 E 0.0049 0.9484 0.0467 107 L 0.0052 0.9428 0.0520 108 Y 0.0057 0.9386 0.0556 109 E 0.0064 0.9184 0.0752 110 V 0.0075 0.8831 0.1094 111 A 0.0098 0.8484 0.1418 112 S 0.0091 0.8734 0.1175 113 D 0.0060 0.8915 0.1025 114 F 0.0062 0.9074 0.0863 115 A 0.0059 0.9203 0.0738 116 I 0.0053 0.9325 0.0622 117 E 0.0056 0.9413 0.0532 118 R 0.0050 0.9448 0.0502 119 E 0.0049 0.9453 0.0498 120 K 0.0051 0.9419 0.0530 121 Q 0.0053 0.9325 0.0622 122 L 0.0057 0.9148 0.0796 123 L 0.0074 0.8405 0.1521 124 E 0.0117 0.5701 0.4181 125 E 0.0171 0.2392 0.7436 126 F 0.0599 0.0509 0.8893 127 E 0.0454 0.0259 0.9287 128 E 0.0051 0.9283 0.0667 129 A 0.0048 0.9463 0.0489 130 E 0.0048 0.9532 0.0420 131 K 0.0047 0.9596 0.0358 132 D 0.0047 0.9563 0.0390 133 Q 0.0047 0.9556 0.0397 134 L 0.0047 0.9568 0.0385 135 F 0.0047 0.9590 0.0363 136 I 0.0047 0.9583 0.0369 137 L 0.0047 0.9572 0.0381 138 L 0.0047 0.9586 0.0367 139 K 0.0047 0.9585 0.0368 140 K 0.0047 0.9568 0.0385 141 L 0.0047 0.9555 0.0398 142 R 0.0049 0.9508 0.0443 143 N 0.0056 0.9189 0.0756 144 K 0.0083 0.8679 0.1238 145 V 0.0219 0.8122 0.1658 146 D 0.0110 0.6863 0.3027 147 Q 0.0156 0.5355 0.4489 148 M 0.0399 0.1625 0.7977