# This file is the result of combining several RDB files, specifically # T0356.t06.dssp-ebghstl.rdb (weight 1.53986) # T0356.t06.stride-ebghtl.rdb (weight 1.24869) # T0356.t06.str2.rdb (weight 1.54758) # T0356.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 T0356.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 56.258 # # ============================================ # Comments from T0356.t06.stride-ebghtl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 56.258 # # ============================================ # Comments from T0356.t06.str2.rdb # ============================================ # TARGET T0356 # 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 T0356.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 56.258 # # ============================================ # Comments from T0356.t06.alpha.rdb # ============================================ # TARGET T0356 # 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 T0356.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 56.258 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0344 0.1112 0.8543 2 D 0.0480 0.1890 0.7629 3 A 0.0491 0.2672 0.6837 4 M 0.0742 0.1411 0.7848 5 K 0.0700 0.1492 0.7808 6 Y 0.0417 0.4243 0.5340 7 N 0.0335 0.4181 0.5484 8 D 0.0519 0.3876 0.5605 9 L 0.0049 0.9339 0.0612 10 R 0.0047 0.9562 0.0391 11 D 0.0047 0.9555 0.0398 12 F 0.0047 0.9603 0.0350 13 L 0.0047 0.9601 0.0352 14 T 0.0046 0.9600 0.0353 15 L 0.0047 0.9595 0.0359 16 L 0.0047 0.9551 0.0402 17 E 0.0048 0.9250 0.0702 18 Q 0.0073 0.7939 0.1988 19 Q 0.0448 0.3073 0.6479 20 G 0.0245 0.0302 0.9453 21 E 0.0937 0.0310 0.8753 22 L 0.6137 0.0146 0.3717 23 K 0.8190 0.0121 0.1688 24 R 0.9003 0.0057 0.0940 25 I 0.8567 0.0089 0.1343 26 T 0.6399 0.0452 0.3148 27 L 0.4260 0.0112 0.5628 28 P 0.2908 0.0134 0.6958 29 V 0.1958 0.0247 0.7795 30 D 0.1078 0.0189 0.8733 31 P 0.0094 0.5173 0.4733 32 H 0.0128 0.6214 0.3658 33 L 0.0232 0.7837 0.1931 34 E 0.0300 0.8381 0.1320 35 I 0.0091 0.9263 0.0645 36 T 0.0054 0.9511 0.0434 37 E 0.0052 0.9546 0.0402 38 I 0.0055 0.9543 0.0402 39 A 0.0047 0.9503 0.0449 40 D 0.0048 0.9467 0.0485 41 R 0.0048 0.9477 0.0474 42 T 0.0054 0.9447 0.0499 43 L 0.0077 0.9293 0.0630 44 R 0.0113 0.8694 0.1193 45 A 0.0423 0.4061 0.5516 46 G 0.0299 0.0302 0.9399 47 G 0.0546 0.0152 0.9302 48 P 0.1570 0.0208 0.8222 49 A 0.4846 0.0416 0.4738 50 L 0.6530 0.0563 0.2907 51 L 0.7588 0.0525 0.1887 52 F 0.6741 0.0454 0.2805 53 E 0.5032 0.0714 0.4253 54 N 0.1943 0.0211 0.7846 55 P 0.0677 0.1336 0.7986 56 K 0.0428 0.1579 0.7994 57 G 0.0449 0.1553 0.7999 58 Y 0.0843 0.0977 0.8180 59 S 0.1190 0.0679 0.8131 60 M 0.2025 0.0455 0.7521 61 P 0.3192 0.0468 0.6340 62 V 0.7321 0.0683 0.1996 63 L 0.7834 0.0878 0.1288 64 C 0.7229 0.1114 0.1657 65 N 0.5855 0.1363 0.2782 66 L 0.3845 0.1729 0.4426 67 F 0.2315 0.1212 0.6473 68 G 0.1216 0.0661 0.8123 69 T 0.0708 0.0329 0.8963 70 P 0.0062 0.9206 0.0732 71 K 0.0049 0.9450 0.0501 72 R 0.0053 0.9508 0.0439 73 V 0.0072 0.9469 0.0460 74 A 0.0097 0.9247 0.0657 75 M 0.0116 0.8553 0.1332 76 G 0.0201 0.7322 0.2477 77 M 0.0541 0.3885 0.5574 78 G 0.0428 0.0620 0.8953 79 Q 0.0612 0.0773 0.8614 80 E 0.0636 0.1233 0.8131 81 D 0.0724 0.1805 0.7471 82 V 0.0129 0.8028 0.1843 83 S 0.0081 0.8850 0.1069 84 A 0.0057 0.9249 0.0693 85 L 0.0052 0.9415 0.0534 86 R 0.0050 0.9511 0.0439 87 E 0.0050 0.9510 0.0440 88 V 0.0047 0.9530 0.0423 89 G 0.0047 0.9536 0.0417 90 K 0.0047 0.9528 0.0425 91 L 0.0048 0.9500 0.0452 92 L 0.0048 0.9429 0.0523 93 A 0.0052 0.8935 0.1013 94 F 0.0065 0.8160 0.1775 95 L 0.0367 0.5916 0.3717 96 K 0.0325 0.3504 0.6171 97 E 0.0634 0.0620 0.8746 98 P 0.0604 0.0385 0.9011 99 E 0.0637 0.0283 0.9080 100 P 0.0540 0.0216 0.9245 101 P 0.0549 0.1321 0.8131 102 K 0.0380 0.3772 0.5848 103 G 0.0517 0.4038 0.5445 104 F 0.0222 0.7989 0.1790 105 R 0.0114 0.8885 0.1000 106 D 0.0142 0.8899 0.0959 107 L 0.0057 0.9171 0.0772 108 F 0.0075 0.8913 0.1012 109 D 0.0071 0.8114 0.1814 110 K 0.0109 0.6824 0.3067 111 L 0.0299 0.3538 0.6164 112 P 0.0098 0.7388 0.2514 113 Q 0.0145 0.7995 0.1859 114 F 0.0142 0.8616 0.1242 115 K 0.0177 0.8607 0.1217 116 Q 0.0218 0.8180 0.1602 117 V 0.0262 0.7365 0.2373 118 L 0.0667 0.4482 0.4851 119 N 0.0567 0.0981 0.8452 120 M 0.0736 0.0181 0.9083 121 P 0.1016 0.0202 0.8782 122 T 0.2307 0.0942 0.6751 123 K 0.4486 0.1480 0.4034 124 R 0.6144 0.1330 0.2526 125 L 0.4796 0.1057 0.4147 126 R 0.1939 0.0992 0.7069 127 G 0.0835 0.0501 0.8664 128 A 0.1439 0.0400 0.8161 129 P 0.2721 0.0557 0.6722 130 C 0.4616 0.0936 0.4448 131 Q 0.5806 0.0915 0.3279 132 Q 0.6890 0.0748 0.2362 133 K 0.7444 0.0683 0.1872 134 I 0.7499 0.0526 0.1975 135 V 0.6458 0.0621 0.2921 136 S 0.3271 0.0683 0.6047 137 G 0.0893 0.0479 0.8628 138 D 0.0819 0.0923 0.8258 139 D 0.2297 0.0547 0.7157 140 V 0.3269 0.0231 0.6500 141 D 0.2454 0.0215 0.7331 142 L 0.0344 0.6830 0.2826 143 N 0.0277 0.5705 0.4017 144 R 0.0532 0.5109 0.4359 145 I 0.1411 0.0328 0.8260 146 P 0.1756 0.0318 0.7926 147 I 0.2890 0.0568 0.6542 148 M 0.3413 0.0622 0.5965 149 T 0.3854 0.0746 0.5400 150 C 0.3216 0.0457 0.6326 151 W 0.1029 0.0214 0.8757 152 P 0.0157 0.2120 0.7723 153 E 0.0215 0.1660 0.8126 154 D 0.0717 0.1928 0.7355 155 A 0.1213 0.2000 0.6786 156 A 0.1494 0.2262 0.6244 157 P 0.1807 0.2963 0.5230 158 L 0.3676 0.2344 0.3979 159 I 0.5003 0.0923 0.4074 160 T 0.4469 0.0629 0.4902 161 W 0.3035 0.1348 0.5617 162 G 0.3589 0.0981 0.5430 163 L 0.6620 0.0683 0.2697 164 T 0.7991 0.0507 0.1502 165 V 0.8223 0.0411 0.1367 166 T 0.7460 0.0309 0.2231 167 R 0.5615 0.0335 0.4050 168 G 0.2042 0.0157 0.7801 169 P 0.0398 0.1040 0.8562 170 H 0.0453 0.0944 0.8603 171 K 0.0786 0.1115 0.8099 172 E 0.1146 0.0735 0.8119 173 R 0.4469 0.0366 0.5164 174 Q 0.6405 0.0328 0.3267 175 N 0.6797 0.0253 0.2951 176 L 0.6764 0.0380 0.2856 177 G 0.7404 0.0306 0.2290 178 I 0.7575 0.0301 0.2124 179 Y 0.5822 0.0262 0.3917 180 R 0.1982 0.0237 0.7781