# This file is the result of combining several RDB files, specifically # T0137.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0137.t2k.stride-ebghtl.rdb (weight 1.24869) # T0137.t2k.str.rdb (weight 1.53983) # T0137.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 T0137.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0137 # 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 T0137.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 111 # # ============================================ # Comments from T0137.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0137 # 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 T0137.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 111 # # ============================================ # Comments from T0137.t2k.str.rdb # ============================================ # TARGET T0137 # 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 T0137.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 111 # # ============================================ # Comments from T0137.t2k.alpha.rdb # ============================================ # TARGET T0137 # 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 T0137.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 111 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0591 0.0382 0.9028 2 E 0.1303 0.0710 0.7987 3 A 0.1793 0.0839 0.7369 4 F 0.3461 0.0590 0.5949 5 L 0.4286 0.0364 0.5350 6 G 0.6341 0.0166 0.3493 7 T 0.7919 0.0113 0.1968 8 W 0.8622 0.0089 0.1289 9 K 0.8701 0.0110 0.1190 10 M 0.8366 0.0175 0.1459 11 E 0.7053 0.0394 0.2553 12 K 0.6202 0.0437 0.3361 13 S 0.3473 0.0799 0.5728 14 E 0.2051 0.1406 0.6543 15 G 0.1942 0.1490 0.6569 16 F 0.0125 0.8307 0.1568 17 D 0.0054 0.9379 0.0566 18 K 0.0047 0.9506 0.0447 19 I 0.0045 0.9542 0.0413 20 M 0.0046 0.9534 0.0420 21 E 0.0048 0.9455 0.0497 22 R 0.0057 0.8964 0.0979 23 L 0.0438 0.3583 0.5980 24 G 0.0355 0.0231 0.9415 25 V 0.0621 0.0181 0.9198 26 D 0.0508 0.0739 0.8753 27 F 0.0082 0.9037 0.0881 28 V 0.0064 0.9367 0.0568 29 T 0.0096 0.9408 0.0497 30 R 0.0154 0.9336 0.0510 31 K 0.0145 0.9284 0.0571 32 M 0.0137 0.9153 0.0711 33 G 0.0235 0.8656 0.1110 34 N 0.0304 0.7362 0.2334 35 L 0.0669 0.4677 0.4654 36 V 0.1187 0.1739 0.7075 37 K 0.1208 0.0368 0.8424 38 P 0.1981 0.0345 0.7674 39 N 0.5866 0.0258 0.3876 40 L 0.8952 0.0055 0.0992 41 I 0.9193 0.0037 0.0770 42 V 0.9181 0.0036 0.0783 43 T 0.8735 0.0069 0.1195 44 D 0.5709 0.0133 0.4158 45 L 0.1452 0.0633 0.7916 46 G 0.0800 0.0443 0.8757 47 G 0.0600 0.0596 0.8804 48 G 0.1412 0.0447 0.8140 49 K 0.7521 0.0105 0.2374 50 Y 0.8786 0.0040 0.1174 51 K 0.9127 0.0039 0.0834 52 M 0.9150 0.0038 0.0811 53 R 0.8864 0.0074 0.1062 54 S 0.8236 0.0051 0.1713 55 E 0.6323 0.0126 0.3550 56 S 0.4560 0.0156 0.5283 57 T 0.3017 0.0364 0.6619 58 F 0.3568 0.0278 0.6155 59 K 0.4910 0.0240 0.4850 60 T 0.6159 0.0114 0.3726 61 T 0.8234 0.0077 0.1688 62 E 0.8854 0.0040 0.1106 63 C 0.8919 0.0041 0.1040 64 S 0.8801 0.0043 0.1157 65 F 0.8615 0.0050 0.1336 66 K 0.7693 0.0077 0.2229 67 L 0.4968 0.0452 0.4579 68 G 0.2014 0.0551 0.7435 69 E 0.3790 0.0411 0.5799 70 K 0.5981 0.0319 0.3701 71 F 0.6747 0.0339 0.2914 72 K 0.7293 0.0274 0.2433 73 E 0.7299 0.0315 0.2386 74 V 0.7831 0.0192 0.1977 75 T 0.4373 0.0294 0.5333 76 P 0.1597 0.0502 0.7901 77 D 0.0555 0.0252 0.9193 78 S 0.0452 0.0437 0.9110 79 R 0.3706 0.0153 0.6141 80 E 0.8184 0.0058 0.1758 81 V 0.8589 0.0061 0.1349 82 A 0.8806 0.0082 0.1113 83 S 0.9025 0.0047 0.0928 84 L 0.9189 0.0038 0.0773 85 I 0.9217 0.0039 0.0743 86 T 0.9045 0.0045 0.0910 87 V 0.7880 0.0136 0.1984 88 E 0.2958 0.0575 0.6466 89 N 0.0481 0.0230 0.9289 90 G 0.0534 0.0399 0.9068 91 V 0.7604 0.0073 0.2323 92 M 0.9179 0.0035 0.0786 93 K 0.9120 0.0062 0.0818 94 H 0.9234 0.0045 0.0721 95 E 0.9145 0.0060 0.0795 96 Q 0.8902 0.0059 0.1039 97 D 0.6872 0.0273 0.2855 98 D 0.2877 0.0366 0.6758 99 K 0.0969 0.0647 0.8384 100 T 0.1006 0.0458 0.8536 101 K 0.2644 0.0393 0.6964 102 V 0.5977 0.0119 0.3904 103 T 0.8212 0.0060 0.1728 104 Y 0.8941 0.0043 0.1016 105 I 0.9127 0.0040 0.0833 106 E 0.9204 0.0036 0.0761 107 R 0.9142 0.0043 0.0815 108 V 0.9131 0.0044 0.0825 109 V 0.8865 0.0058 0.1077 110 E 0.5888 0.0215 0.3897 111 G 0.0632 0.0212 0.9157 112 N 0.1051 0.0408 0.8541 113 E 0.7973 0.0070 0.1956 114 L 0.9195 0.0035 0.0770 115 K 0.9220 0.0044 0.0737 116 A 0.9315 0.0035 0.0650 117 T 0.9293 0.0036 0.0671 118 V 0.9206 0.0040 0.0754 119 K 0.8933 0.0051 0.1016 120 V 0.7509 0.0192 0.2299 121 D 0.0766 0.0360 0.8873 122 E 0.1135 0.0289 0.8576 123 V 0.8320 0.0050 0.1630 124 V 0.8982 0.0072 0.0946 125 C 0.9100 0.0055 0.0845 126 V 0.9132 0.0054 0.0813 127 R 0.8801 0.0106 0.1093 128 T 0.8532 0.0145 0.1323 129 Y 0.8146 0.0172 0.1682 130 S 0.7610 0.0271 0.2119 131 K 0.6379 0.0259 0.3362 132 V 0.3039 0.0216 0.6745 133 A 0.0531 0.0174 0.9295