# This file is the result of combining several RDB files, specifically # T0316.t04.dssp-ebghstl.rdb (weight 1.53986) # T0316.t04.stride-ebghtl.rdb (weight 1.24869) # T0316.t04.str2.rdb (weight 1.54758) # T0316.t04.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 T0316.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0316.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1276 # # ============================================ # Comments from T0316.t04.stride-ebghtl.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0316.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1276 # # ============================================ # Comments from T0316.t04.str2.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0316.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1276 # # ============================================ # Comments from T0316.t04.alpha.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0316.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1276 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0728 0.0180 0.9093 2 S 0.1003 0.0436 0.8561 3 D 0.0711 0.1388 0.7901 4 N 0.0545 0.2046 0.7409 5 S 0.0634 0.1665 0.7701 6 K 0.0632 0.0823 0.8545 7 T 0.1581 0.0274 0.8145 8 R 0.7388 0.0046 0.2565 9 V 0.9213 0.0034 0.0753 10 V 0.9330 0.0032 0.0638 11 V 0.9310 0.0036 0.0654 12 G 0.9173 0.0057 0.0770 13 M 0.8529 0.0086 0.1385 14 S 0.5549 0.0152 0.4300 15 G 0.1793 0.0313 0.7894 16 G 0.0966 0.0608 0.8426 17 V 0.0675 0.3412 0.5913 18 D 0.0343 0.5967 0.3690 19 S 0.0060 0.9229 0.0711 20 S 0.0049 0.9541 0.0410 21 V 0.0047 0.9594 0.0359 22 T 0.0047 0.9601 0.0353 23 A 0.0046 0.9613 0.0341 24 L 0.0047 0.9614 0.0339 25 L 0.0047 0.9609 0.0344 26 L 0.0047 0.9601 0.0353 27 K 0.0049 0.9553 0.0398 28 E 0.0060 0.9214 0.0726 29 Q 0.0418 0.3987 0.5595 30 G 0.0391 0.0189 0.9420 31 Y 0.0690 0.0136 0.9174 32 D 0.3137 0.0175 0.6687 33 V 0.7280 0.0072 0.2647 34 I 0.8300 0.0129 0.1571 35 G 0.9100 0.0041 0.0858 36 I 0.9112 0.0046 0.0842 37 F 0.9031 0.0061 0.0908 38 M 0.8528 0.0088 0.1384 39 K 0.7703 0.0221 0.2076 40 N 0.6566 0.0234 0.3200 41 W 0.4463 0.0444 0.5093 42 D 0.3261 0.0456 0.6283 43 D 0.2272 0.1031 0.6698 44 T 0.1608 0.0743 0.7649 45 D 0.0749 0.1410 0.7840 46 E 0.0551 0.1621 0.7828 47 N 0.0963 0.1108 0.7928 48 G 0.0836 0.0664 0.8500 49 V 0.2131 0.0760 0.7109 50 C 0.2304 0.0629 0.7067 51 T 0.1193 0.0623 0.8184 52 A 0.0741 0.1074 0.8186 53 T 0.0363 0.5174 0.4462 54 E 0.0371 0.6238 0.3390 55 D 0.0409 0.6212 0.3380 56 Y 0.0061 0.9326 0.0613 57 K 0.0048 0.9559 0.0393 58 D 0.0047 0.9577 0.0376 59 V 0.0047 0.9594 0.0359 60 V 0.0046 0.9614 0.0340 61 A 0.0046 0.9613 0.0341 62 V 0.0046 0.9615 0.0339 63 A 0.0047 0.9603 0.0350 64 D 0.0048 0.9534 0.0418 65 Q 0.0055 0.9257 0.0688 66 I 0.0447 0.4660 0.4893 67 G 0.0457 0.0133 0.9410 68 I 0.0653 0.0079 0.9268 69 P 0.2414 0.0098 0.7489 70 Y 0.8530 0.0057 0.1412 71 Y 0.9080 0.0045 0.0875 72 S 0.9225 0.0037 0.0738 73 V 0.8419 0.0117 0.1464 74 N 0.4752 0.0066 0.5182 75 F 0.0795 0.4138 0.5067 76 E 0.0299 0.6489 0.3211 77 K 0.0119 0.8503 0.1378 78 E 0.0140 0.8884 0.0976 79 Y 0.0113 0.9074 0.0813 80 W 0.0069 0.9339 0.0592 81 D 0.0062 0.9343 0.0595 82 R 0.0067 0.9312 0.0621 83 V 0.0081 0.9249 0.0670 84 F 0.0101 0.9219 0.0680 85 E 0.0099 0.9254 0.0647 86 Y 0.0122 0.9138 0.0740 87 F 0.0122 0.9029 0.0849 88 L 0.0117 0.9177 0.0706 89 A 0.0059 0.9424 0.0517 90 E 0.0062 0.9387 0.0551 91 Y 0.0109 0.9213 0.0678 92 R 0.0140 0.8678 0.1182 93 A 0.0390 0.4944 0.4666 94 G 0.0264 0.0839 0.8897 95 R 0.0776 0.0302 0.8922 96 T 0.1218 0.0128 0.8654 97 P 0.1126 0.0272 0.8602 98 N 0.1035 0.0245 0.8720 99 P 0.0545 0.1777 0.7678 100 D 0.0779 0.2368 0.6853 101 V 0.0943 0.4378 0.4679 102 M 0.1013 0.4010 0.4977 103 C 0.0719 0.3830 0.5451 104 N 0.0339 0.4503 0.5158 105 K 0.0237 0.7428 0.2335 106 E 0.0207 0.8806 0.0987 107 I 0.0325 0.8858 0.0816 108 K 0.0235 0.8969 0.0796 109 F 0.0101 0.9330 0.0568 110 K 0.0070 0.9412 0.0519 111 A 0.0051 0.9534 0.0416 112 F 0.0048 0.9572 0.0380 113 L 0.0047 0.9603 0.0349 114 D 0.0047 0.9611 0.0342 115 Y 0.0047 0.9612 0.0341 116 A 0.0047 0.9608 0.0345 117 I 0.0048 0.9550 0.0402 118 T 0.0051 0.9388 0.0561 119 L 0.0404 0.4385 0.5210 120 G 0.0606 0.0110 0.9284 121 A 0.0859 0.0165 0.8976 122 D 0.0809 0.0541 0.8649 123 Y 0.8690 0.0118 0.1192 124 V 0.9182 0.0074 0.0744 125 A 0.9053 0.0109 0.0837 126 T 0.7550 0.0338 0.2112 127 G 0.3004 0.0508 0.6488 128 H 0.1894 0.1274 0.6832 129 Y 0.1770 0.1923 0.6307 130 A 0.1186 0.3910 0.4905 131 R 0.0779 0.4530 0.4692 132 V 0.0827 0.4248 0.4925 133 A 0.0938 0.2799 0.6263 134 R 0.0728 0.1675 0.7597 135 D 0.0511 0.1354 0.8135 136 E 0.0353 0.1350 0.8297 137 D 0.0443 0.0596 0.8962