# This file is the result of combining several RDB files, specifically # T0331.t06.dssp-ebghstl.rdb (weight 1.53986) # T0331.t06.stride-ebghtl.rdb (weight 1.24869) # T0331.t06.str2.rdb (weight 1.54758) # T0331.t06.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 T0331.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0331 # Using neural net t06-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 T0331.t06-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 16 # # ============================================ # Comments from T0331.t06.stride-ebghtl.rdb # ============================================ # TARGET T0331 # Using neural net t06-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 T0331.t06-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 16 # # ============================================ # Comments from T0331.t06.str2.rdb # ============================================ # TARGET T0331 # Using neural net t06-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 T0331.t06-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 16 # # ============================================ # Comments from T0331.t06.alpha.rdb # ============================================ # TARGET T0331 # Using neural net t06-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 T0331.t06-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 16 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0628 0.0382 0.8990 2 E 0.0795 0.0515 0.8691 3 L 0.0076 0.8910 0.1014 4 K 0.0062 0.9224 0.0714 5 D 0.0062 0.9362 0.0576 6 I 0.0047 0.9556 0.0397 7 M 0.0047 0.9579 0.0374 8 H 0.0048 0.9525 0.0427 9 I 0.0050 0.9352 0.0597 10 L 0.0074 0.9010 0.0916 11 E 0.0078 0.6730 0.3192 12 D 0.0162 0.3196 0.6642 13 M 0.0832 0.0547 0.8621 14 K 0.0912 0.0507 0.8581 15 V 0.6098 0.0165 0.3738 16 G 0.8165 0.0099 0.1737 17 V 0.9180 0.0036 0.0783 18 F 0.9169 0.0048 0.0782 19 A 0.8933 0.0065 0.1002 20 T 0.8487 0.0061 0.1451 21 L 0.6354 0.0331 0.3314 22 D 0.2835 0.0719 0.6447 23 E 0.0906 0.1376 0.7719 24 Y 0.0746 0.0728 0.8525 25 G 0.0728 0.0284 0.8988 26 N 0.1290 0.0197 0.8512 27 P 0.2751 0.0524 0.6725 28 H 0.4564 0.0556 0.4880 29 A 0.6096 0.0392 0.3512 30 R 0.5963 0.0312 0.3725 31 H 0.6069 0.0865 0.3067 32 A 0.5930 0.0887 0.3182 33 H 0.6566 0.0723 0.2711 34 I 0.7564 0.0546 0.1890 35 T 0.8119 0.0471 0.1411 36 A 0.7852 0.0627 0.1521 37 A 0.6237 0.1229 0.2534 38 N 0.3957 0.1327 0.4716 39 E 0.1008 0.1225 0.7767 40 E 0.1230 0.0299 0.8472 41 G 0.4662 0.0150 0.5188 42 I 0.8777 0.0043 0.1180 43 F 0.9225 0.0038 0.0737 44 F 0.9130 0.0047 0.0823 45 M 0.8858 0.0051 0.1090 46 T 0.6448 0.0105 0.3447 47 S 0.1281 0.0294 0.8425 48 P 0.0171 0.1163 0.8667 49 E 0.0307 0.1008 0.8685 50 T 0.0645 0.1618 0.7737 51 H 0.0726 0.3769 0.5505 52 F 0.0764 0.6973 0.2264 53 Y 0.0262 0.8701 0.1037 54 D 0.0131 0.9095 0.0774 55 Q 0.0142 0.9110 0.0747 56 L 0.0190 0.8664 0.1145 57 M 0.0258 0.6894 0.2848 58 G 0.0311 0.3283 0.6406 59 D 0.0684 0.0446 0.8869 60 Q 0.0649 0.0716 0.8634 61 R 0.2375 0.0473 0.7152 62 V 0.8010 0.0067 0.1923 63 A 0.9016 0.0039 0.0944 64 M 0.9210 0.0032 0.0758 65 T 0.9028 0.0048 0.0924 66 A 0.8806 0.0048 0.1146 67 I 0.7716 0.0107 0.2177 68 S 0.3283 0.0163 0.6554 69 E 0.0540 0.1164 0.8296 70 E 0.0486 0.0590 0.8925 71 G 0.1037 0.0643 0.8320 72 Y 0.3889 0.0481 0.5629 73 L 0.6747 0.0315 0.2937 74 I 0.6687 0.0434 0.2880 75 Q 0.7663 0.0283 0.2054 76 V 0.8798 0.0134 0.1068 77 V 0.9138 0.0054 0.0808 78 R 0.9149 0.0041 0.0810 79 V 0.8835 0.0067 0.1098 80 E 0.7632 0.0305 0.2063 81 G 0.7494 0.0075 0.2431 82 T 0.8088 0.0062 0.1850 83 A 0.8004 0.0057 0.1939 84 R 0.7778 0.0077 0.2145 85 P 0.7445 0.0089 0.2466 86 V 0.3948 0.0338 0.5714 87 E 0.2209 0.0509 0.7282 88 N 0.0917 0.1728 0.7355 89 D 0.0198 0.6626 0.3176 90 Y 0.0429 0.7483 0.2088 91 L 0.0854 0.7803 0.1343 92 K 0.0857 0.7921 0.1222 93 T 0.0739 0.8324 0.0937 94 V 0.0435 0.8699 0.0865 95 F 0.0397 0.8268 0.1335 96 A 0.0241 0.7015 0.2744 97 D 0.0249 0.4924 0.4827 98 N 0.0837 0.1498 0.7665 99 P 0.0150 0.5075 0.4774 100 Y 0.0607 0.5046 0.4348 101 Y 0.0844 0.6657 0.2499 102 Q 0.0745 0.7450 0.1805 103 H 0.1232 0.6932 0.1835 104 I 0.1800 0.6205 0.1995 105 Y 0.3203 0.4145 0.2652 106 K 0.2572 0.2999 0.4429 107 D 0.1054 0.0996 0.7950 108 E 0.0322 0.1679 0.8000 109 S 0.0363 0.1037 0.8600 110 S 0.0672 0.0611 0.8718 111 D 0.0654 0.0885 0.8460 112 T 0.5053 0.0507 0.4440 113 M 0.8217 0.0064 0.1719 114 Q 0.8966 0.0060 0.0973 115 V 0.9224 0.0047 0.0729 116 F 0.9055 0.0104 0.0841 117 Q 0.9169 0.0060 0.0771 118 I 0.8767 0.0212 0.1021 119 Y 0.7879 0.0213 0.1907 120 A 0.4153 0.0621 0.5226 121 G 0.2638 0.0559 0.6803 122 H 0.7150 0.0353 0.2497 123 G 0.8303 0.0165 0.1531 124 F 0.8760 0.0141 0.1099 125 Y 0.8596 0.0230 0.1174 126 H 0.7521 0.0399 0.2079 127 S 0.6089 0.0265 0.3645 128 L 0.3136 0.0706 0.6158 129 T 0.1792 0.0584 0.7624 130 Q 0.0873 0.0885 0.8242 131 G 0.1061 0.0597 0.8341 132 H 0.3478 0.0412 0.6109 133 K 0.6280 0.0227 0.3493 134 Y 0.8036 0.0146 0.1818 135 I 0.8700 0.0136 0.1165 136 F 0.8557 0.0143 0.1301 137 S 0.7979 0.0173 0.1848 138 I 0.5581 0.0458 0.3961 139 G 0.2419 0.0458 0.7124 140 Q 0.0908 0.0884 0.8208 141 G 0.0837 0.1246 0.7917 142 E 0.1180 0.1747 0.7073 143 H 0.0966 0.3145 0.5889 144 S 0.0852 0.4347 0.4801 145 E 0.1108 0.5696 0.3196 146 V 0.1417 0.5623 0.2960 147 R 0.1589 0.4272 0.4140 148 A 0.1198 0.2664 0.6138 149 L 0.0435 0.0690 0.8874