# This file is the result of combining several RDB files, specifically # T0324.t04.dssp-ebghstl.rdb (weight 1.53986) # T0324.t04.stride-ebghtl.rdb (weight 1.24869) # T0324.t04.str2.rdb (weight 1.54758) # T0324.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 T0324.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0324 # 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 T0324.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 2280 # # ============================================ # Comments from T0324.t04.stride-ebghtl.rdb # ============================================ # TARGET T0324 # 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 T0324.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 2280 # # ============================================ # Comments from T0324.t04.str2.rdb # ============================================ # TARGET T0324 # 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 T0324.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 2280 # # ============================================ # Comments from T0324.t04.alpha.rdb # ============================================ # TARGET T0324 # 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 T0324.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 2280 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0653 0.0113 0.9234 2 T 0.1877 0.0154 0.7969 3 Y 0.2971 0.0066 0.6963 4 Q 0.4087 0.0338 0.5574 5 A 0.9213 0.0036 0.0751 6 L 0.9326 0.0032 0.0642 7 M 0.9331 0.0032 0.0637 8 F 0.9156 0.0039 0.0805 9 D 0.6735 0.0055 0.3210 10 I 0.2458 0.0567 0.6975 11 D 0.0900 0.0572 0.8528 12 G 0.0928 0.0639 0.8433 13 T 0.2760 0.0660 0.6581 14 L 0.5318 0.0749 0.3933 15 T 0.3776 0.1073 0.5151 16 N 0.2121 0.0787 0.7092 17 S 0.0590 0.1178 0.8232 18 Q 0.0317 0.5695 0.3989 19 P 0.0064 0.9181 0.0755 20 A 0.0053 0.9425 0.0521 21 Y 0.0048 0.9544 0.0408 22 T 0.0047 0.9595 0.0359 23 T 0.0047 0.9605 0.0348 24 V 0.0047 0.9600 0.0354 25 M 0.0047 0.9607 0.0346 26 R 0.0047 0.9608 0.0345 27 E 0.0047 0.9602 0.0351 28 V 0.0047 0.9594 0.0359 29 L 0.0048 0.9572 0.0380 30 A 0.0052 0.9503 0.0445 31 T 0.0099 0.8984 0.0917 32 Y 0.0459 0.5390 0.4150 33 G 0.0326 0.0319 0.9355 34 K 0.0529 0.0128 0.9343 35 P 0.1007 0.0156 0.8837 36 F 0.1125 0.0108 0.8766 37 S 0.0601 0.0095 0.9304 38 P 0.0051 0.9260 0.0689 39 A 0.0047 0.9511 0.0442 40 Q 0.0049 0.9495 0.0456 41 A 0.0059 0.9396 0.0545 42 Q 0.0069 0.9111 0.0820 43 K 0.0083 0.8193 0.1724 44 T 0.0178 0.6970 0.2852 45 F 0.0591 0.2587 0.6822 46 P 0.0342 0.1890 0.7767 47 M 0.0422 0.3437 0.6140 48 A 0.0455 0.4694 0.4851 49 A 0.0065 0.9017 0.0918 50 E 0.0053 0.9496 0.0450 51 Q 0.0050 0.9532 0.0417 52 A 0.0053 0.9535 0.0412 53 M 0.0051 0.9501 0.0447 54 T 0.0052 0.9380 0.0568 55 E 0.0063 0.8797 0.1140 56 L 0.0448 0.5604 0.3948 57 G 0.0381 0.0839 0.8780 58 I 0.0648 0.0616 0.8736 59 A 0.0705 0.0764 0.8531 60 A 0.0111 0.7584 0.2305 61 S 0.0092 0.7844 0.2064 62 E 0.0112 0.7947 0.1941 63 F 0.0093 0.8532 0.1374 64 D 0.0056 0.9050 0.0894 65 H 0.0056 0.9272 0.0672 66 F 0.0056 0.9312 0.0632 67 Q 0.0051 0.9468 0.0481 68 A 0.0048 0.9511 0.0441 69 Q 0.0052 0.9464 0.0485 70 Y 0.0048 0.9538 0.0414 71 E 0.0047 0.9560 0.0392 72 D 0.0047 0.9564 0.0389 73 V 0.0048 0.9505 0.0447 74 M 0.0051 0.9437 0.0512 75 A 0.0054 0.9096 0.0850 76 S 0.0065 0.8141 0.1793 77 H 0.0113 0.6756 0.3131 78 Y 0.0468 0.3857 0.5675 79 D 0.0198 0.3695 0.6107 80 Q 0.0405 0.2855 0.6740 81 I 0.2028 0.0973 0.6999 82 E 0.3179 0.0770 0.6051 83 L 0.3149 0.0569 0.6282 84 Y 0.0997 0.0375 0.8628 85 P 0.0189 0.3050 0.6761 86 G 0.0195 0.3316 0.6489 87 I 0.0189 0.7971 0.1840 88 T 0.0138 0.9136 0.0726 89 S 0.0140 0.9282 0.0578 90 L 0.0066 0.9408 0.0525 91 F 0.0075 0.9247 0.0678 92 E 0.0066 0.8329 0.1605 93 Q 0.0113 0.6383 0.3504 94 L 0.0439 0.2188 0.7373 95 P 0.0291 0.2734 0.6975 96 S 0.0160 0.2927 0.6914 97 E 0.0297 0.1147 0.8555 98 L 0.2663 0.0130 0.7207 99 R 0.5433 0.0261 0.4306 100 L 0.9228 0.0048 0.0724 101 G 0.9311 0.0035 0.0654 102 I 0.9314 0.0034 0.0652 103 V 0.8854 0.0057 0.1089 104 T 0.4261 0.0133 0.5607 105 S 0.0634 0.0622 0.8744 106 Q 0.0417 0.1797 0.7786 107 R 0.0444 0.3472 0.6084 108 R 0.0127 0.7964 0.1910 109 N 0.0083 0.8835 0.1083 110 E 0.0087 0.9072 0.0841 111 L 0.0098 0.9204 0.0698 112 E 0.0097 0.9260 0.0643 113 S 0.0082 0.9261 0.0656 114 G 0.0087 0.9087 0.0825 115 M 0.0136 0.8667 0.1197 116 R 0.0106 0.7523 0.2371 117 S 0.0145 0.5842 0.4013 118 Y 0.0626 0.1965 0.7409 119 P 0.0436 0.1628 0.7936 120 F 0.0824 0.3236 0.5940 121 M 0.1251 0.3524 0.5226 122 M 0.1494 0.3485 0.5021 123 R 0.2480 0.1998 0.5522 124 M 0.4440 0.0289 0.5271 125 A 0.3803 0.0606 0.5591 126 V 0.8878 0.0084 0.1039 127 T 0.9197 0.0066 0.0737 128 I 0.9053 0.0087 0.0861 129 S 0.6930 0.0096 0.2974 130 A 0.1357 0.2427 0.6216 131 D 0.0427 0.2883 0.6690 132 D 0.0620 0.3118 0.6262 133 T 0.0937 0.0971 0.8091 134 P 0.0625 0.1461 0.7915 135 K 0.0671 0.1378 0.7951 136 R 0.1014 0.0796 0.8190 137 K 0.0853 0.0228 0.8919 138 P 0.0883 0.0253 0.8863 139 D 0.0965 0.0185 0.8850 140 P 0.0173 0.7833 0.1995 141 L 0.0070 0.9330 0.0600 142 P 0.0049 0.9526 0.0425 143 L 0.0048 0.9569 0.0383 144 L 0.0047 0.9606 0.0348 145 T 0.0047 0.9607 0.0347 146 A 0.0047 0.9601 0.0352 147 L 0.0047 0.9589 0.0364 148 E 0.0050 0.9503 0.0448 149 K 0.0060 0.9097 0.0842 150 V 0.0462 0.4213 0.5325 151 N 0.0446 0.0162 0.9392 152 V 0.0673 0.0083 0.9244 153 A 0.0764 0.0109 0.9127 154 P 0.0527 0.5881 0.3592 155 Q 0.0655 0.5810 0.3534 156 N 0.1456 0.4161 0.4383 157 A 0.8385 0.0167 0.1448 158 L 0.9033 0.0088 0.0879 159 F 0.9199 0.0048 0.0753 160 I 0.8518 0.0264 0.1219 161 G 0.5368 0.0210 0.4421 162 D 0.1883 0.0214 0.7902 163 S 0.0846 0.0626 0.8528 164 V 0.0267 0.4933 0.4800 165 S 0.0282 0.6024 0.3694 166 D 0.0194 0.6656 0.3150 167 E 0.0048 0.9509 0.0443 168 Q 0.0047 0.9566 0.0387 169 T 0.0047 0.9597 0.0356 170 A 0.0047 0.9592 0.0362 171 Q 0.0048 0.9526 0.0425 172 A 0.0057 0.9096 0.0847 173 A 0.0454 0.4279 0.5267 174 N 0.0481 0.0184 0.9336 175 V 0.0927 0.0072 0.9001 176 D 0.2617 0.0336 0.7047 177 F 0.9054 0.0043 0.0903 178 G 0.9279 0.0036 0.0685 179 L 0.9287 0.0035 0.0677 180 A 0.8936 0.0054 0.1010 181 V 0.6103 0.0110 0.3787 182 W 0.2482 0.0378 0.7140 183 G 0.0909 0.0415 0.8677 184 M 0.1034 0.0373 0.8594 185 D 0.0852 0.0261 0.8887 186 P 0.0388 0.1667 0.7945 187 N 0.0409 0.2478 0.7113 188 A 0.0374 0.3783 0.5843 189 D 0.0483 0.3757 0.5759 190 H 0.0682 0.3280 0.6038 191 Q 0.0961 0.2144 0.6895 192 K 0.1778 0.1153 0.7069 193 V 0.2947 0.0626 0.6426 194 A 0.4033 0.0873 0.5093 195 H 0.8044 0.0452 0.1505 196 R 0.8359 0.0380 0.1261 197 F 0.7168 0.0253 0.2579 198 Q 0.3012 0.0574 0.6414 199 K 0.1224 0.0149 0.8627 200 P 0.0080 0.8559 0.1361 201 L 0.0061 0.8989 0.0951 202 D 0.0064 0.9164 0.0772 203 I 0.0059 0.9327 0.0614 204 L 0.0056 0.9365 0.0579 205 E 0.0061 0.9112 0.0827 206 L 0.0084 0.8087 0.1828 207 F 0.0314 0.5490 0.4196 208 K 0.0171 0.1618 0.8211