# This file is the result of combining several RDB files, specifically # T0222.t04.dssp-ebghstl.rdb (weight 1.53986) # T0222.t04.stride-ebghtl.rdb (weight 1.24869) # T0222.t04.str2.rdb (weight 1.54758) # T0222.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 T0222.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0222 # Using neural net t04-2621-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 T0222.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 1 # # ============================================ # Comments from T0222.t04.stride-ebghtl.rdb # ============================================ # TARGET T0222 # 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 T0222.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 1 # # ============================================ # Comments from T0222.t04.str2.rdb # ============================================ # TARGET T0222 # 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 T0222.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 1 # # ============================================ # Comments from T0222.t04.alpha.rdb # ============================================ # TARGET T0222 # 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 T0222.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 Q 0.1085 0.1762 0.7153 2 G 0.1120 0.1080 0.7800 3 I 0.1863 0.0663 0.7474 4 T 0.2193 0.0676 0.7131 5 K 0.1982 0.0537 0.7482 6 P 0.1776 0.1060 0.7165 7 V 0.1464 0.3023 0.5513 8 S 0.1149 0.3973 0.4878 9 E 0.0558 0.7157 0.2285 10 K 0.0737 0.6825 0.2438 11 L 0.1254 0.5809 0.2937 12 L 0.1175 0.4079 0.4747 13 G 0.0724 0.1650 0.7626 14 S 0.0969 0.1502 0.7529 15 S 0.1517 0.1747 0.6736 16 Y 0.2292 0.1787 0.5921 17 K 0.2678 0.1736 0.5586 18 T 0.3438 0.1870 0.4692 19 T 0.3835 0.2480 0.3685 20 T 0.4406 0.2623 0.2971 21 A 0.4257 0.3284 0.2459 22 I 0.4223 0.3592 0.2185 23 E 0.2989 0.4344 0.2667 24 G 0.2138 0.3679 0.4183 25 E 0.3244 0.4013 0.2742 26 I 0.4135 0.3845 0.2019 27 R 0.3391 0.3987 0.2622 28 N 0.2681 0.4048 0.3271 29 F 0.2707 0.3906 0.3387 30 A 0.3328 0.3275 0.3397 31 Y 0.3881 0.2936 0.3182 32 R 0.2965 0.2391 0.4644 33 G 0.2700 0.1337 0.5963 34 I 0.5235 0.0947 0.3818 35 F 0.6363 0.0558 0.3078 36 T 0.5205 0.0514 0.4281 37 T 0.3640 0.0677 0.5683 38 A 0.2892 0.0486 0.6622 39 P 0.3731 0.0796 0.5472 40 I 0.3368 0.1151 0.5481 41 Q 0.3130 0.1073 0.5797 42 K 0.1685 0.1327 0.6989 43 G 0.1275 0.0956 0.7770 44 E 0.2647 0.1026 0.6328 45 A 0.4362 0.1070 0.4569 46 F 0.3537 0.0783 0.5679 47 S 0.2047 0.0742 0.7211 48 E 0.1001 0.3984 0.5015 49 D 0.0915 0.2689 0.6396 50 N 0.1882 0.2144 0.5974 51 I 0.5822 0.0798 0.3380 52 A 0.7398 0.0573 0.2029 53 V 0.7870 0.0439 0.1691 54 L 0.6911 0.0335 0.2754 55 R 0.2876 0.0225 0.6899 56 P 0.0473 0.1067 0.8460 57 G 0.0358 0.0738 0.8904 58 Q 0.1720 0.0595 0.7685 59 K 0.1386 0.0263 0.8351 60 P 0.1073 0.1237 0.7689 61 Q 0.0561 0.1788 0.7651 62 G 0.0576 0.1289 0.8134 63 L 0.1144 0.0726 0.8131 64 H 0.1080 0.0497 0.8423 65 P 0.0354 0.6624 0.3022 66 R 0.0381 0.7726 0.1893 67 F 0.0384 0.8523 0.1093 68 F 0.0510 0.8592 0.0899 69 E 0.0645 0.8409 0.0946 70 L 0.0882 0.8026 0.1092 71 L 0.0833 0.7677 0.1490 72 T 0.0908 0.6535 0.2557 73 S 0.0616 0.4763 0.4620 74 G 0.0838 0.2980 0.6183 75 V 0.2929 0.2656 0.4414 76 R 0.4732 0.2396 0.2872 77 A 0.5369 0.2504 0.2127 78 V 0.4883 0.2523 0.2594 79 R 0.4468 0.1842 0.3690 80 D 0.3764 0.1174 0.5062 81 I 0.2609 0.0289 0.7102 82 P 0.1605 0.0320 0.8074 83 A 0.0633 0.2575 0.6793 84 D 0.0549 0.2486 0.6965 85 T 0.0896 0.2213 0.6890 86 G 0.1750 0.1106 0.7145 87 I 0.4790 0.0755 0.4455 88 V 0.5999 0.0893 0.3108 89 W 0.4542 0.1907 0.3550 90 D 0.2798 0.3034 0.4168 91 D 0.2032 0.3930 0.4038 92 I 0.3617 0.3468 0.2915 93 L 0.4684 0.2897 0.2420 94 L 0.4171 0.2418 0.3411 95 K 0.2506 0.1882 0.5612 96 D 0.1323 0.0896 0.7782 97 S 0.1119 0.0515 0.8366 98 P 0.0768 0.1851 0.7382 99 F 0.0982 0.1938 0.7080 100 H 0.1122 0.1359 0.7518 101 E 0.0814 0.1136 0.8050