# This file is the result of combining several RDB files, specifically # T0129.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0129.t2k.stride-ebghtl.rdb (weight 1.24869) # T0129.t2k.str.rdb (weight 1.53983) # T0129.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 T0129.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0129 # 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 T0129.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 6 # # ============================================ # Comments from T0129.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0129 # 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 T0129.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 6 # # ============================================ # Comments from T0129.t2k.str.rdb # ============================================ # TARGET T0129 # 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 T0129.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 6 # # ============================================ # Comments from T0129.t2k.alpha.rdb # ============================================ # TARGET T0129 # 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 T0129.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 6 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0411 0.0573 0.9016 2 L 0.0990 0.1373 0.7637 3 I 0.0702 0.2662 0.6637 4 S 0.0563 0.3218 0.6219 5 H 0.0335 0.4899 0.4766 6 S 0.0096 0.7920 0.1983 7 D 0.0079 0.8597 0.1324 8 L 0.0055 0.9119 0.0826 9 N 0.0054 0.9219 0.0727 10 Q 0.0052 0.9106 0.0842 11 Q 0.0049 0.9089 0.0861 12 L 0.0066 0.8846 0.1088 13 K 0.0059 0.8361 0.1581 14 S 0.0083 0.7598 0.2320 15 A 0.0282 0.5669 0.4049 16 G 0.0409 0.2236 0.7355 17 I 0.0613 0.1578 0.7809 18 G 0.0979 0.1027 0.7994 19 F 0.0998 0.0421 0.8581 20 N 0.0757 0.0495 0.8749 21 A 0.0078 0.9113 0.0809 22 T 0.0058 0.9279 0.0663 23 E 0.0103 0.9259 0.0638 24 L 0.0113 0.9234 0.0653 25 H 0.0141 0.8741 0.1118 26 G 0.0238 0.8028 0.1734 27 F 0.0450 0.8097 0.1453 28 L 0.0847 0.7601 0.1551 29 S 0.0639 0.6753 0.2608 30 G 0.1157 0.4269 0.4574 31 L 0.2549 0.3927 0.3524 32 L 0.3176 0.3122 0.3702 33 C 0.2396 0.2076 0.5528 34 G 0.1253 0.0968 0.7779 35 G 0.0626 0.0736 0.8638 36 L 0.0670 0.1479 0.7851 37 K 0.0510 0.1502 0.7988 38 D 0.0348 0.4266 0.5386 39 Q 0.0149 0.6444 0.3407 40 S 0.0157 0.7513 0.2330 41 W 0.0069 0.9046 0.0885 42 L 0.0073 0.9216 0.0711 43 P 0.0076 0.9357 0.0567 44 L 0.0059 0.9445 0.0497 45 L 0.0074 0.9417 0.0508 46 Y 0.0078 0.9340 0.0583 47 Q 0.0106 0.9026 0.0868 48 F 0.0173 0.8025 0.1802 49 S 0.0473 0.4958 0.4569 50 N 0.0426 0.2969 0.6605 51 D 0.0341 0.2253 0.7407 52 N 0.0422 0.1570 0.8007 53 H 0.0848 0.1312 0.7839 54 A 0.1290 0.1523 0.7188 55 Y 0.0950 0.1757 0.7292 56 P 0.0322 0.5970 0.3708 57 T 0.0128 0.8126 0.1746 58 G 0.0149 0.8421 0.1430 59 L 0.0107 0.8694 0.1199 60 V 0.0112 0.8768 0.1120 61 Q 0.0088 0.8883 0.1029 62 P 0.0081 0.9074 0.0845 63 V 0.0048 0.9416 0.0536 64 T 0.0045 0.9489 0.0466 65 E 0.0046 0.9449 0.0504 66 L 0.0045 0.9460 0.0494 67 Y 0.0048 0.9461 0.0492 68 E 0.0046 0.9415 0.0539 69 Q 0.0049 0.9330 0.0622 70 I 0.0069 0.9220 0.0710 71 S 0.0072 0.9082 0.0846 72 Q 0.0089 0.8823 0.1089 73 T 0.0118 0.8323 0.1559 74 L 0.0360 0.6858 0.2782 75 S 0.0443 0.5533 0.4023 76 D 0.0709 0.3079 0.6212 77 V 0.0670 0.1591 0.7738 78 E 0.0898 0.0669 0.8433 79 G 0.2829 0.0340 0.6831 80 F 0.6924 0.0076 0.3000 81 T 0.8783 0.0056 0.1162 82 F 0.9133 0.0036 0.0832 83 E 0.9074 0.0043 0.0883 84 L 0.8826 0.0044 0.1130 85 G 0.7906 0.0073 0.2021 86 L 0.4468 0.0070 0.5461 87 T 0.1868 0.0167 0.7966 88 E 0.0481 0.0864 0.8655 89 D 0.0273 0.0580 0.9148 90 E 0.0722 0.1064 0.8215 91 N 0.0942 0.1756 0.7302 92 V 0.0855 0.4859 0.4286 93 F 0.0695 0.6137 0.3167 94 T 0.0743 0.6464 0.2792 95 Q 0.0278 0.7857 0.1865 96 A 0.0107 0.8666 0.1227 97 D 0.0059 0.9018 0.0924 98 S 0.0056 0.9120 0.0824 99 L 0.0045 0.9492 0.0463 100 S 0.0045 0.9542 0.0413 101 D 0.0045 0.9526 0.0428 102 W 0.0045 0.9508 0.0447 103 A 0.0046 0.9458 0.0496 104 N 0.0047 0.9323 0.0630 105 Q 0.0054 0.9156 0.0789 106 F 0.0077 0.8993 0.0930 107 L 0.0158 0.8501 0.1340 108 L 0.0208 0.7725 0.2067 109 G 0.0257 0.6179 0.3564 110 I 0.0586 0.4701 0.4713 111 G 0.0754 0.3049 0.6197 112 L 0.1215 0.2938 0.5847 113 A 0.1394 0.2227 0.6379 114 Q 0.1013 0.3319 0.5669 115 P 0.0503 0.5081 0.4416 116 E 0.0535 0.5019 0.4445 117 L 0.0453 0.5758 0.3789 118 A 0.0360 0.4968 0.4672 119 K 0.0469 0.4602 0.4929 120 E 0.0724 0.4526 0.4750 121 K 0.0712 0.4508 0.4779 122 G 0.0776 0.4692 0.4532 123 E 0.0828 0.6093 0.3079 124 I 0.0181 0.8791 0.1028 125 G 0.0097 0.9124 0.0778 126 E 0.0093 0.9154 0.0753 127 A 0.0059 0.9336 0.0605 128 V 0.0055 0.9403 0.0542 129 D 0.0051 0.9358 0.0590 130 D 0.0114 0.9100 0.0786 131 L 0.0053 0.9392 0.0555 132 Q 0.0047 0.9490 0.0463 133 D 0.0048 0.9401 0.0551 134 I 0.0056 0.9341 0.0603 135 C 0.0093 0.8910 0.0997 136 Q 0.0074 0.7930 0.1995 137 L 0.0444 0.4986 0.4570 138 G 0.0455 0.1245 0.8300 139 Y 0.0679 0.0661 0.8660 140 D 0.0911 0.0589 0.8499 141 E 0.0183 0.5270 0.4547 142 D 0.0206 0.4788 0.5006 143 D 0.0268 0.4608 0.5124 144 N 0.0525 0.2969 0.6506 145 E 0.0066 0.8460 0.1474 146 E 0.0054 0.8786 0.1160 147 E 0.0053 0.8871 0.1076 148 L 0.0047 0.9110 0.0843 149 A 0.0049 0.9197 0.0754 150 E 0.0050 0.9209 0.0741 151 A 0.0047 0.9154 0.0799 152 L 0.0044 0.9416 0.0539 153 E 0.0044 0.9519 0.0437 154 E 0.0044 0.9548 0.0408 155 I 0.0044 0.9575 0.0381 156 I 0.0044 0.9603 0.0353 157 E 0.0044 0.9603 0.0353 158 Y 0.0044 0.9584 0.0372 159 V 0.0044 0.9587 0.0369 160 R 0.0044 0.9594 0.0362 161 T 0.0044 0.9586 0.0370 162 I 0.0044 0.9588 0.0368 163 A 0.0045 0.9581 0.0374 164 M 0.0049 0.9554 0.0397 165 L 0.0056 0.9460 0.0484 166 F 0.0082 0.9165 0.0753 167 Y 0.0158 0.8546 0.1297 168 S 0.0245 0.7351 0.2404 169 H 0.0388 0.5784 0.3828 170 F 0.0681 0.2811 0.6508 171 N 0.0599 0.0865 0.8536 172 E 0.0609 0.0494 0.8897 173 G 0.0829 0.0417 0.8754 174 E 0.1008 0.0345 0.8647 175 I 0.1010 0.0539 0.8451 176 E 0.0859 0.0628 0.8513 177 S 0.1096 0.0599 0.8305 178 K 0.0872 0.0385 0.8743 179 P 0.1174 0.0388 0.8438 180 V 0.1822 0.0569 0.7609 181 L 0.1472 0.0493 0.8035 182 H 0.0658 0.0154 0.9188