# This file is the result of combining several RDB files, specifically # T0212.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0212.t2k.stride-ebghtl.rdb (weight 1.24869) # T0212.t2k.str2.rdb (weight 1.54758) # T0212.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 T0212.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0212 # 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 T0212.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 53 # # ============================================ # Comments from T0212.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0212 # 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 T0212.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 53 # # ============================================ # Comments from T0212.t2k.str2.rdb # ============================================ # TARGET T0212 # 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 T0212.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 53 # # ============================================ # Comments from T0212.t2k.alpha.rdb # ============================================ # TARGET T0212 # 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 T0212.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 53 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1165 0.0371 0.8463 2 S 0.2973 0.0444 0.6583 3 A 0.3989 0.0563 0.5447 4 L 0.4296 0.0611 0.5093 5 D 0.2604 0.0477 0.6919 6 N 0.1107 0.0712 0.8181 7 S 0.1852 0.0287 0.7861 8 I 0.6630 0.0054 0.3316 9 R 0.8681 0.0034 0.1285 10 V 0.9120 0.0036 0.0843 11 E 0.9188 0.0034 0.0778 12 V 0.8970 0.0039 0.0991 13 K 0.8215 0.0054 0.1732 14 T 0.6957 0.0123 0.2920 15 E 0.4905 0.0479 0.4615 16 Y 0.4582 0.0416 0.5001 17 I 0.3230 0.0582 0.6188 18 E 0.1781 0.2104 0.6115 19 Q 0.1186 0.3565 0.5249 20 Q 0.1214 0.3080 0.5706 21 S 0.1313 0.1742 0.6945 22 S 0.1027 0.1067 0.7906 23 P 0.0486 0.3254 0.6259 24 E 0.0451 0.3282 0.6267 25 D 0.0692 0.2573 0.6735 26 E 0.1235 0.0893 0.7872 27 K 0.4736 0.0248 0.5016 28 Y 0.8659 0.0071 0.1270 29 L 0.9157 0.0037 0.0805 30 F 0.9180 0.0048 0.0772 31 S 0.9158 0.0033 0.0809 32 Y 0.9088 0.0041 0.0871 33 T 0.9159 0.0033 0.0808 34 I 0.9207 0.0032 0.0761 35 T 0.9192 0.0045 0.0763 36 I 0.9100 0.0067 0.0833 37 I 0.8316 0.0273 0.1411 38 N 0.6440 0.0228 0.3333 39 L 0.1960 0.0445 0.7595 40 G 0.0751 0.0549 0.8701 41 E 0.0858 0.0871 0.8271 42 Q 0.2006 0.1011 0.6983 43 A 0.3746 0.1465 0.4789 44 A 0.5481 0.2013 0.2505 45 K 0.7004 0.1539 0.1457 46 L 0.7598 0.1165 0.1237 47 E 0.7262 0.1024 0.1714 48 T 0.7273 0.0695 0.2032 49 R 0.6909 0.0665 0.2426 50 H 0.7642 0.0259 0.2099 51 W 0.8477 0.0133 0.1390 52 I 0.8857 0.0081 0.1062 53 I 0.8828 0.0097 0.1075 54 T 0.8492 0.0080 0.1427 55 D 0.3309 0.0205 0.6485 56 A 0.0335 0.1113 0.8552 57 N 0.0493 0.0216 0.9291 58 G 0.0502 0.0305 0.9193 59 K 0.3787 0.0146 0.6067 60 T 0.8368 0.0059 0.1574 61 S 0.8352 0.0165 0.1483 62 E 0.8665 0.0090 0.1245 63 V 0.8049 0.0131 0.1820 64 Q 0.6692 0.0269 0.3038 65 G 0.3993 0.0343 0.5664 66 A 0.2639 0.0763 0.6598 67 G 0.3034 0.0894 0.6071 68 V 0.4019 0.1079 0.4902 69 V 0.3165 0.1043 0.5792 70 G 0.2170 0.0663 0.7167 71 E 0.2493 0.0583 0.6925 72 T 0.3128 0.0244 0.6628 73 P 0.2799 0.0327 0.6874 74 T 0.3854 0.0371 0.5775 75 I 0.3649 0.0161 0.6190 76 P 0.1135 0.0186 0.8679 77 P 0.0297 0.0731 0.8971 78 N 0.0353 0.0453 0.9194 79 T 0.2506 0.0212 0.7283 80 A 0.6900 0.0087 0.3013 81 Y 0.8652 0.0064 0.1284 82 Q 0.8896 0.0056 0.1048 83 Y 0.8468 0.0087 0.1445 84 T 0.6703 0.0210 0.3087 85 S 0.5000 0.0351 0.4649 86 G 0.4502 0.0360 0.5138 87 T 0.5489 0.0156 0.4355 88 V 0.5051 0.0173 0.4776 89 L 0.3275 0.0255 0.6470 90 D 0.2322 0.0296 0.7382 91 T 0.1200 0.0180 0.8620 92 P 0.1313 0.0544 0.8143 93 F 0.2678 0.0488 0.6834 94 G 0.5183 0.0353 0.4465 95 I 0.6848 0.0207 0.2945 96 M 0.7853 0.0139 0.2008 97 Y 0.7805 0.0139 0.2056 98 G 0.7665 0.0122 0.2213 99 T 0.8694 0.0063 0.1243 100 Y 0.8876 0.0079 0.1045 101 G 0.9132 0.0042 0.0826 102 M 0.9012 0.0050 0.0938 103 V 0.8914 0.0052 0.1034 104 S 0.6026 0.0095 0.3879 105 E 0.0538 0.1089 0.8374 106 S 0.0495 0.0193 0.9312 107 G 0.1116 0.0277 0.8607 108 E 0.5308 0.0086 0.4605 109 H 0.8918 0.0037 0.1045 110 F 0.8812 0.0058 0.1130 111 N 0.8922 0.0049 0.1029 112 A 0.8305 0.0056 0.1639 113 I 0.7402 0.0067 0.2531 114 I 0.5273 0.0081 0.4646 115 K 0.2860 0.0208 0.6932 116 P 0.2033 0.0743 0.7223 117 F 0.4130 0.0759 0.5111 118 R 0.4268 0.0943 0.4789 119 L 0.3085 0.1234 0.5682 120 A 0.2102 0.1168 0.6731 121 T 0.1180 0.0685 0.8135 122 P 0.0596 0.3361 0.6042 123 G 0.0595 0.4015 0.5390 124 L 0.0763 0.4169 0.5068 125 L 0.0772 0.2175 0.7052 126 H 0.0505 0.0453 0.9042