# This file is the result of combining several RDB files, specifically # T0132.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0132.t2k.stride-ebghtl.rdb (weight 1.24869) # T0132.t2k.str.rdb (weight 1.53983) # T0132.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 T0132.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0132 # 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 T0132.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 89 # # ============================================ # Comments from T0132.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0132 # 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 T0132.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 89 # # ============================================ # Comments from T0132.t2k.str.rdb # ============================================ # TARGET T0132 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0132.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 89 # # ============================================ # Comments from T0132.t2k.alpha.rdb # ============================================ # TARGET T0132 # 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 T0132.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 89 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0666 0.0314 0.9019 2 S 0.1596 0.0719 0.7685 3 A 0.1924 0.0960 0.7116 4 N 0.1925 0.1009 0.7066 5 F 0.1831 0.0706 0.7463 6 T 0.1541 0.0516 0.7943 7 D 0.1469 0.0816 0.7716 8 K 0.1772 0.0695 0.7532 9 N 0.3211 0.0889 0.5900 10 G 0.4257 0.0578 0.5166 11 R 0.4611 0.0400 0.4988 12 Q 0.2887 0.0452 0.6661 13 S 0.2109 0.0538 0.7354 14 K 0.0847 0.1015 0.8137 15 G 0.1602 0.0608 0.7790 16 V 0.6501 0.0180 0.3319 17 L 0.8653 0.0046 0.1301 18 L 0.8919 0.0056 0.1025 19 L 0.9065 0.0042 0.0893 20 R 0.8857 0.0066 0.1077 21 T 0.8475 0.0072 0.1453 22 L 0.7997 0.0070 0.1933 23 A 0.6619 0.0125 0.3255 24 M 0.3719 0.0165 0.6116 25 P 0.1449 0.2069 0.6482 26 S 0.0549 0.3512 0.5939 27 D 0.0761 0.3777 0.5462 28 T 0.1595 0.1607 0.6798 29 N 0.0984 0.1073 0.7943 30 A 0.0452 0.2508 0.7040 31 N 0.0565 0.2114 0.7321 32 G 0.0915 0.2387 0.6697 33 D 0.2627 0.3610 0.3763 34 I 0.3413 0.4245 0.2341 35 F 0.1875 0.5428 0.2697 36 G 0.0691 0.7310 0.1999 37 G 0.0242 0.8348 0.1410 38 W 0.0081 0.9453 0.0466 39 I 0.0053 0.9516 0.0431 40 M 0.0044 0.9499 0.0456 41 S 0.0045 0.9478 0.0478 42 Q 0.0046 0.9448 0.0507 43 M 0.0045 0.9472 0.0483 44 D 0.0045 0.9524 0.0430 45 M 0.0045 0.9557 0.0398 46 G 0.0044 0.9575 0.0381 47 G 0.0044 0.9587 0.0369 48 A 0.0044 0.9601 0.0356 49 I 0.0044 0.9602 0.0354 50 L 0.0044 0.9590 0.0366 51 A 0.0045 0.9558 0.0398 52 K 0.0050 0.9470 0.0480 53 E 0.0083 0.9033 0.0885 54 I 0.0196 0.7889 0.1915 55 A 0.0522 0.3849 0.5630 56 H 0.0324 0.1169 0.8507 57 G 0.0655 0.0519 0.8826 58 R 0.2478 0.0280 0.7242 59 V 0.6608 0.0112 0.3280 60 V 0.8597 0.0108 0.1295 61 T 0.9052 0.0078 0.0870 62 V 0.8800 0.0125 0.1075 63 A 0.8493 0.0117 0.1391 64 V 0.7113 0.0565 0.2322 65 E 0.3935 0.1239 0.4826 66 S 0.4486 0.1139 0.4374 67 M 0.7802 0.0117 0.2081 68 N 0.8124 0.0120 0.1756 69 F 0.8038 0.0140 0.1822 70 I 0.7229 0.0254 0.2518 71 K 0.5578 0.0120 0.4302 72 P 0.5608 0.0087 0.4305 73 I 0.5937 0.0075 0.3989 74 S 0.3827 0.0132 0.6041 75 V 0.1280 0.0862 0.7857 76 G 0.0449 0.0515 0.9036 77 D 0.2767 0.0275 0.6958 78 V 0.8144 0.0039 0.1816 79 V 0.9152 0.0039 0.0809 80 C 0.9258 0.0039 0.0703 81 C 0.9202 0.0041 0.0756 82 Y 0.9010 0.0085 0.0905 83 G 0.8952 0.0060 0.0987 84 Q 0.9093 0.0048 0.0859 85 C 0.9134 0.0037 0.0829 86 L 0.8560 0.0171 0.1268 87 K 0.8356 0.0090 0.1553 88 V 0.5485 0.0317 0.4198 89 G 0.2764 0.0354 0.6882 90 R 0.2905 0.0318 0.6777 91 S 0.5601 0.0119 0.4280 92 S 0.8175 0.0044 0.1781 93 I 0.9087 0.0040 0.0874 94 K 0.9271 0.0033 0.0696 95 I 0.9170 0.0039 0.0791 96 K 0.9279 0.0034 0.0688 97 V 0.9268 0.0037 0.0695 98 E 0.9260 0.0035 0.0705 99 V 0.9108 0.0039 0.0853 100 W 0.8775 0.0084 0.1141 101 V 0.7458 0.0303 0.2240 102 K 0.4721 0.0815 0.4463 103 K 0.3358 0.0968 0.5674 104 V 0.2665 0.1698 0.5636 105 A 0.1893 0.1791 0.6315 106 S 0.1595 0.1310 0.7095 107 E 0.0887 0.1255 0.7859 108 P 0.0856 0.1238 0.7906 109 I 0.1139 0.1267 0.7594 110 G 0.1559 0.0978 0.7464 111 E 0.3520 0.1204 0.5276 112 R 0.5593 0.1016 0.3391 113 Y 0.6957 0.0657 0.2386 114 C 0.7803 0.0488 0.1709 115 V 0.7883 0.0412 0.1705 116 T 0.8216 0.0309 0.1476 117 D 0.8755 0.0134 0.1111 118 A 0.8993 0.0068 0.0939 119 V 0.9198 0.0043 0.0759 120 F 0.9257 0.0040 0.0703 121 T 0.9232 0.0040 0.0728 122 F 0.9169 0.0040 0.0791 123 V 0.8988 0.0044 0.0968 124 A 0.8420 0.0053 0.1527 125 V 0.7705 0.0081 0.2214 126 D 0.2105 0.0146 0.7749 127 N 0.0167 0.1195 0.8638 128 N 0.0476 0.0223 0.9301 129 G 0.0467 0.0329 0.9204 130 R 0.1748 0.0116 0.8136 131 S 0.5892 0.0077 0.4031 132 R 0.3882 0.0108 0.6010 133 T 0.3228 0.0149 0.6623 134 I 0.2065 0.0232 0.7703 135 P 0.1510 0.0349 0.8141 136 R 0.1210 0.0522 0.8268 137 E 0.1327 0.0519 0.8154 138 N 0.2193 0.0411 0.7396 139 N 0.1960 0.0240 0.7800 140 Q 0.1499 0.0321 0.8180 141 E 0.0858 0.0320 0.8822 142 L 0.0587 0.0541 0.8873 143 E 0.0056 0.9010 0.0934 144 K 0.0046 0.9230 0.0724 145 A 0.0046 0.9404 0.0550 146 L 0.0051 0.9398 0.0551 147 A 0.0062 0.9258 0.0680 148 L 0.0062 0.9177 0.0761 149 I 0.0096 0.8703 0.1201 150 S 0.0103 0.8134 0.1763 151 E 0.0185 0.6551 0.3264 152 Q 0.0426 0.4170 0.5404 153 P 0.0514 0.2783 0.6703 154 L 0.0360 0.0599 0.9040