# This file is the result of combining several RDB files, specifically # T0224.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0224.t2k.stride-ebghtl.rdb (weight 1.24869) # T0224.t2k.str2.rdb (weight 1.54758) # T0224.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 T0224.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0224 # 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 T0224.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 22 # # ============================================ # Comments from T0224.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0224 # 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 T0224.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 22 # # ============================================ # Comments from T0224.t2k.str2.rdb # ============================================ # TARGET T0224 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0224.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 22 # # ============================================ # Comments from T0224.t2k.alpha.rdb # ============================================ # TARGET T0224 # 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 T0224.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 22 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1279 0.0409 0.8312 2 A 0.4184 0.0555 0.5261 3 L 0.7047 0.0481 0.2472 4 V 0.7640 0.0689 0.1671 5 L 0.7267 0.0661 0.2071 6 V 0.6060 0.0709 0.3231 7 K 0.3601 0.0821 0.5578 8 Y 0.1474 0.0426 0.8099 9 G 0.0753 0.1204 0.8042 10 T 0.0673 0.1418 0.7909 11 D 0.0527 0.1884 0.7589 12 H 0.0373 0.3326 0.6301 13 P 0.0313 0.4404 0.5284 14 V 0.0322 0.6859 0.2818 15 E 0.0138 0.8848 0.1014 16 K 0.0086 0.9157 0.0757 17 L 0.0073 0.9278 0.0650 18 K 0.0080 0.9261 0.0658 19 I 0.0106 0.9112 0.0782 20 R 0.0143 0.8231 0.1626 21 S 0.0233 0.6598 0.3169 22 A 0.1138 0.2499 0.6363 23 K 0.0660 0.0702 0.8638 24 A 0.0192 0.2547 0.7261 25 E 0.0224 0.1422 0.8354 26 D 0.1083 0.1182 0.7735 27 K 0.4634 0.0616 0.4751 28 I 0.8482 0.0186 0.1332 29 V 0.8874 0.0214 0.0912 30 L 0.8610 0.0311 0.1079 31 I 0.6513 0.0625 0.2861 32 Q 0.2954 0.1495 0.5552 33 N 0.1566 0.2325 0.6109 34 G 0.4318 0.2500 0.3181 35 V 0.5813 0.2706 0.1480 36 F 0.6049 0.2944 0.1008 37 W 0.5912 0.3007 0.1081 38 A 0.5273 0.3236 0.1491 39 L 0.4667 0.3046 0.2287 40 E 0.2804 0.2357 0.4839 41 E 0.1586 0.1014 0.7400 42 L 0.1493 0.0786 0.7721 43 E 0.1438 0.0969 0.7593 44 T 0.1188 0.0593 0.8219 45 P 0.1237 0.0525 0.8237 46 A 0.2843 0.0269 0.6888 47 K 0.5646 0.0229 0.4126 48 V 0.8715 0.0107 0.1178 49 Y 0.8950 0.0095 0.0954 50 A 0.8575 0.0114 0.1311 51 I 0.5947 0.0509 0.3543 52 K 0.1533 0.3926 0.4541 53 D 0.0321 0.6837 0.2842 54 D 0.0344 0.7268 0.2388 55 F 0.0385 0.8070 0.1545 56 L 0.0392 0.7974 0.1634 57 A 0.0432 0.7137 0.2431 58 R 0.0627 0.4522 0.4851 59 G 0.0767 0.2359 0.6874 60 Y 0.0738 0.3948 0.5314 61 S 0.0646 0.5509 0.3845 62 E 0.0409 0.5750 0.3840 63 E 0.0686 0.5113 0.4201 64 D 0.0908 0.3515 0.5577 65 S 0.0419 0.2242 0.7339 66 K 0.0667 0.0907 0.8426 67 V 0.1672 0.0180 0.8148 68 P 0.5062 0.0101 0.4837 69 L 0.8568 0.0049 0.1383 70 I 0.8444 0.0085 0.1472 71 T 0.5592 0.0089 0.4319 72 Y 0.0620 0.6118 0.3263 73 S 0.0205 0.7261 0.2534 74 E 0.0141 0.8160 0.1699 75 F 0.0165 0.8941 0.0894 76 I 0.0149 0.9217 0.0635 77 D 0.0169 0.9200 0.0630 78 L 0.0121 0.9168 0.0710 79 L 0.0189 0.8977 0.0834 80 E 0.0181 0.8733 0.1086 81 G 0.0206 0.7706 0.2089 82 E 0.0390 0.5869 0.3741 83 E 0.0444 0.5135 0.4421 84 K 0.0396 0.5028 0.4577 85 F 0.0719 0.4119 0.5162 86 I 0.0805 0.2246 0.6949 87 G 0.0419 0.0700 0.8881