# This file is the result of combining several RDB files, specifically # T0176.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0176.t2k.stride-ebghtl.rdb (weight 1.24869) # T0176.t2k.str.rdb (weight 1.53983) # T0176.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 T0176.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0176 # 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 T0176.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 31 # # ============================================ # Comments from T0176.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0176 # 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 T0176.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 31 # # ============================================ # Comments from T0176.t2k.str.rdb # ============================================ # TARGET T0176 # 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 T0176.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 31 # # ============================================ # Comments from T0176.t2k.alpha.rdb # ============================================ # TARGET T0176 # 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 T0176.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 31 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0437 0.0827 0.8735 2 D 0.0620 0.1674 0.7706 3 G 0.0783 0.2134 0.7083 4 V 0.0735 0.4173 0.5092 5 M 0.0760 0.4672 0.4567 6 S 0.1088 0.5187 0.3724 7 A 0.2115 0.4778 0.3107 8 V 0.3779 0.3700 0.2521 9 T 0.5451 0.2558 0.1991 10 V 0.5863 0.1729 0.2408 11 N 0.3842 0.1345 0.4812 12 D 0.0636 0.0980 0.8384 13 D 0.0481 0.0463 0.9056 14 G 0.3757 0.0240 0.6003 15 L 0.8309 0.0045 0.1647 16 V 0.9141 0.0035 0.0824 17 L 0.9263 0.0035 0.0702 18 R 0.9293 0.0034 0.0673 19 L 0.9235 0.0037 0.0728 20 Y 0.9134 0.0038 0.0827 21 I 0.8314 0.0058 0.1628 22 Q 0.4449 0.0106 0.5445 23 P 0.1020 0.1034 0.7946 24 K 0.0387 0.0907 0.8705 25 A 0.1153 0.1382 0.7464 26 S 0.1454 0.1481 0.7065 27 R 0.1783 0.2193 0.6025 28 D 0.1637 0.1809 0.6553 29 S 0.2593 0.1216 0.6191 30 I 0.4236 0.0936 0.4828 31 V 0.4012 0.1060 0.4928 32 G 0.3392 0.0839 0.5769 33 L 0.2417 0.0702 0.6881 34 H 0.1759 0.0582 0.7658 35 G 0.0983 0.1155 0.7862 36 D 0.1368 0.1081 0.7551 37 E 0.6139 0.0279 0.3582 38 V 0.8544 0.0045 0.1411 39 K 0.9014 0.0039 0.0947 40 V 0.9165 0.0040 0.0795 41 A 0.8986 0.0042 0.0972 42 I 0.8138 0.0062 0.1800 43 T 0.5476 0.0159 0.4366 44 A 0.2075 0.0100 0.7825 45 P 0.0920 0.0118 0.8962 46 P 0.0799 0.0502 0.8699 47 V 0.0682 0.1580 0.7737 48 D 0.0393 0.3470 0.6137 49 G 0.0307 0.4868 0.4825 50 Q 0.0252 0.8017 0.1731 51 A 0.0159 0.8651 0.1191 52 N 0.0052 0.9173 0.0776 53 S 0.0046 0.9523 0.0431 54 H 0.0044 0.9555 0.0401 55 L 0.0044 0.9589 0.0367 56 V 0.0044 0.9600 0.0356 57 K 0.0044 0.9602 0.0354 58 F 0.0044 0.9602 0.0354 59 L 0.0044 0.9588 0.0368 60 G 0.0045 0.9563 0.0391 61 K 0.0056 0.9379 0.0565 62 Q 0.0096 0.8570 0.1334 63 F 0.0513 0.4787 0.4700 64 R 0.0474 0.0304 0.9222 65 V 0.0864 0.0100 0.9036 66 A 0.1079 0.0161 0.8759 67 K 0.0518 0.4500 0.4982 68 S 0.0664 0.4463 0.4873 69 Q 0.3033 0.3240 0.3727 70 V 0.7325 0.0185 0.2491 71 V 0.8698 0.0083 0.1219 72 I 0.8561 0.0111 0.1328 73 E 0.7088 0.0276 0.2636 74 K 0.3623 0.0355 0.6022 75 G 0.1801 0.0467 0.7732 76 E 0.2083 0.0819 0.7098 77 L 0.2483 0.0807 0.6710 78 G 0.2171 0.0814 0.7015 79 R 0.2109 0.1037 0.6855 80 H 0.3150 0.0713 0.6137 81 K 0.5470 0.0331 0.4200 82 Q 0.7512 0.0110 0.2378 83 I 0.8487 0.0076 0.1437 84 K 0.8520 0.0077 0.1403 85 I 0.6706 0.0140 0.3153 86 I 0.2231 0.0686 0.7083 87 N 0.0808 0.0266 0.8926 88 P 0.0670 0.1045 0.8285 89 Q 0.0842 0.1746 0.7412 90 Q 0.1191 0.2090 0.6719 91 I 0.0944 0.1508 0.7548 92 P 0.0156 0.7428 0.2417 93 P 0.0062 0.9014 0.0924 94 E 0.0066 0.9197 0.0737 95 V 0.0072 0.9202 0.0726 96 A 0.0083 0.9008 0.0909 97 A 0.0111 0.8491 0.1398 98 L 0.0136 0.7315 0.2549 99 I 0.0551 0.4142 0.5307 100 N 0.0408 0.0415 0.9177