# This file is the result of combining several RDB files, specifically # T0362.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0362.t2k.stride-ebghtl.rdb (weight 1.24869) # T0362.t2k.str2.rdb (weight 1.54758) # T0362.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 T0362.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0362 # 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 T0362.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 212 # # ============================================ # Comments from T0362.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0362 # 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 T0362.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 212 # # ============================================ # Comments from T0362.t2k.str2.rdb # ============================================ # TARGET T0362 # 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 T0362.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 212 # # ============================================ # Comments from T0362.t2k.alpha.rdb # ============================================ # TARGET T0362 # 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 T0362.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 212 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0865 0.0335 0.8800 2 N 0.0919 0.0340 0.8741 3 P 0.0790 0.0985 0.8224 4 E 0.0641 0.1153 0.8205 5 N 0.1261 0.0882 0.7858 6 W 0.2877 0.0635 0.6488 7 L 0.5916 0.0270 0.3814 8 L 0.7501 0.0137 0.2363 9 L 0.7604 0.0087 0.2309 10 R 0.7634 0.0079 0.2287 11 R 0.8134 0.0063 0.1803 12 V 0.8763 0.0040 0.1197 13 V 0.8590 0.0038 0.1372 14 R 0.7123 0.0067 0.2810 15 F 0.4016 0.0826 0.5158 16 G 0.1034 0.1657 0.7309 17 D 0.1079 0.1455 0.7466 18 T 0.1732 0.0726 0.7541 19 D 0.1159 0.0532 0.8309 20 A 0.0784 0.3039 0.6177 21 A 0.1494 0.3139 0.5367 22 G 0.2645 0.3742 0.3613 23 V 0.3488 0.4259 0.2252 24 M 0.3605 0.4260 0.2135 25 H 0.1956 0.5318 0.2726 26 F 0.0818 0.6046 0.3135 27 H 0.0175 0.8323 0.1502 28 Q 0.0105 0.8250 0.1645 29 L 0.0068 0.9204 0.0728 30 F 0.0063 0.9364 0.0573 31 R 0.0058 0.9358 0.0584 32 W 0.0052 0.9367 0.0581 33 C 0.0049 0.9458 0.0494 34 H 0.0049 0.9485 0.0466 35 E 0.0050 0.9467 0.0483 36 S 0.0048 0.9479 0.0473 37 W 0.0047 0.9534 0.0419 38 E 0.0047 0.9547 0.0406 39 E 0.0048 0.9496 0.0456 40 S 0.0047 0.9502 0.0451 41 L 0.0049 0.9440 0.0511 42 E 0.0052 0.9361 0.0587 43 S 0.0069 0.8833 0.1099 44 Y 0.0401 0.5176 0.4423 45 G 0.0434 0.1222 0.8344 46 L 0.0642 0.0584 0.8774 47 N 0.1074 0.0877 0.8050 48 P 0.0307 0.7479 0.2214 49 A 0.0257 0.7854 0.1889 50 D 0.0365 0.7674 0.1961 51 I 0.0597 0.6081 0.3322 52 F 0.0670 0.3987 0.5344 53 P 0.0325 0.3955 0.5721 54 G 0.0399 0.3132 0.6469 55 S 0.0586 0.3133 0.6281 56 R 0.0597 0.3614 0.5789 57 K 0.0576 0.3398 0.6026 58 S 0.0914 0.3106 0.5980 59 E 0.1149 0.3414 0.5437 60 V 0.1024 0.2463 0.6513 61 T 0.1218 0.2691 0.6091 62 P 0.1021 0.1955 0.7024 63 E 0.1325 0.0954 0.7720 64 V 0.3689 0.0392 0.5919 65 A 0.5436 0.0188 0.4376 66 L 0.6329 0.0094 0.3577 67 P 0.7566 0.0092 0.2341 68 I 0.8439 0.0085 0.1476 69 I 0.8658 0.0174 0.1167 70 H 0.8804 0.0085 0.1112 71 C 0.8407 0.0190 0.1403 72 Q 0.8466 0.0137 0.1397 73 A 0.7645 0.0196 0.2159 74 D 0.7632 0.0233 0.2135 75 F 0.7416 0.0290 0.2294 76 R 0.6606 0.0369 0.3026 77 R 0.5718 0.0249 0.4033 78 P 0.5551 0.0289 0.4160 79 I 0.6185 0.0233 0.3583 80 H 0.4882 0.0250 0.4868 81 T 0.2283 0.1026 0.6691 82 G 0.0419 0.0703 0.8877 83 D 0.1706 0.0381 0.7914 84 A 0.8163 0.0044 0.1793 85 L 0.9127 0.0036 0.0838 86 A 0.9285 0.0033 0.0683 87 M 0.9258 0.0035 0.0707 88 E 0.9257 0.0033 0.0710 89 L 0.9155 0.0036 0.0808 90 R 0.8854 0.0049 0.1097 91 P 0.8572 0.0081 0.1347 92 E 0.7985 0.0333 0.1682 93 R 0.8025 0.0243 0.1732 94 L 0.5947 0.0318 0.3735 95 N 0.2353 0.0425 0.7222 96 P 0.1803 0.0566 0.7631 97 N 0.6033 0.0220 0.3747 98 S 0.8651 0.0064 0.1285 99 F 0.9079 0.0036 0.0885 100 Q 0.9234 0.0032 0.0734 101 V 0.9139 0.0038 0.0823 102 H 0.9221 0.0032 0.0747 103 F 0.9269 0.0033 0.0698 104 E 0.9278 0.0033 0.0689 105 F 0.9248 0.0034 0.0717 106 R 0.8936 0.0086 0.0978 107 C 0.7384 0.0138 0.2477 108 E 0.1147 0.0305 0.8549 109 E 0.0940 0.0497 0.8563 110 Q 0.7499 0.0095 0.2407 111 I 0.8956 0.0034 0.1010 112 A 0.9079 0.0058 0.0862 113 A 0.9173 0.0049 0.0778 114 H 0.9175 0.0042 0.0783 115 A 0.9009 0.0050 0.0941 116 L 0.9188 0.0038 0.0775 117 I 0.9222 0.0032 0.0746 118 R 0.9248 0.0035 0.0717 119 H 0.9287 0.0031 0.0682 120 L 0.9246 0.0034 0.0720 121 A 0.9185 0.0034 0.0781 122 I 0.8602 0.0066 0.1332 123 N 0.5161 0.0090 0.4749 124 A 0.0261 0.1559 0.8180 125 Q 0.0189 0.1408 0.8403 126 T 0.0609 0.1075 0.8316 127 R 0.0951 0.0415 0.8634 128 H 0.3058 0.0263 0.6679 129 R 0.4284 0.0258 0.5459 130 C 0.3205 0.0311 0.6484 131 A 0.2106 0.0262 0.7631 132 L 0.0768 0.0187 0.9046 133 P 0.0588 0.0502 0.8910 134 E 0.0093 0.7870 0.2038 135 G 0.0065 0.8809 0.1126 136 I 0.0061 0.9097 0.0843 137 D 0.0050 0.9318 0.0631 138 R 0.0053 0.9335 0.0612 139 W 0.0054 0.9344 0.0602 140 L 0.0061 0.9195 0.0744 141 E 0.0059 0.9185 0.0756 142 A 0.0074 0.8703 0.1223 143 S 0.0187 0.7646 0.2167 144 G 0.0353 0.5534 0.4113 145 V 0.0449 0.2910 0.6640 146 G 0.0461 0.1203 0.8336 147 K 0.0744 0.0608 0.8649 148 I 0.1186 0.1590 0.7224 149 G 0.1310 0.1404 0.7286 150 S 0.1719 0.1282 0.6999 151 I 0.1379 0.1109 0.7512