# This file is the result of combining several RDB files, specifically # T0223.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0223.t2k.stride-ebghtl.rdb (weight 1.24869) # T0223.t2k.str2.rdb (weight 1.54758) # T0223.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 T0223.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0223 # 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 T0223.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 69 # # ============================================ # Comments from T0223.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0223 # 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 T0223.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 69 # # ============================================ # Comments from T0223.t2k.str2.rdb # ============================================ # TARGET T0223 # 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 T0223.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 69 # # ============================================ # Comments from T0223.t2k.alpha.rdb # ============================================ # TARGET T0223 # 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 T0223.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 69 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0456 0.1296 0.8248 2 N 0.0832 0.2348 0.6820 3 I 0.0073 0.8804 0.1123 4 F 0.0049 0.9430 0.0521 5 E 0.0049 0.9451 0.0500 6 A 0.0052 0.9424 0.0524 7 I 0.0064 0.9302 0.0634 8 E 0.0080 0.8894 0.1026 9 N 0.0130 0.7285 0.2585 10 R 0.0441 0.5244 0.4314 11 H 0.0605 0.4664 0.4731 12 S 0.0956 0.4726 0.4318 13 V 0.0980 0.5698 0.3322 14 R 0.1306 0.5350 0.3344 15 D 0.1626 0.4043 0.4331 16 F 0.1338 0.2472 0.6189 17 L 0.1034 0.1595 0.7371 18 E 0.0675 0.0912 0.8413 19 R 0.1228 0.0522 0.8250 20 K 0.1619 0.0289 0.8092 21 M 0.1477 0.0264 0.8259 22 P 0.0718 0.0317 0.8964 23 E 0.0061 0.8846 0.1092 24 R 0.0049 0.9161 0.0790 25 V 0.0056 0.9278 0.0666 26 K 0.0047 0.9479 0.0473 27 D 0.0051 0.9436 0.0512 28 D 0.0050 0.9413 0.0537 29 I 0.0048 0.9436 0.0516 30 E 0.0051 0.9474 0.0475 31 N 0.0051 0.9372 0.0578 32 L 0.0061 0.9272 0.0667 33 L 0.0098 0.8795 0.1106 34 V 0.0103 0.7807 0.2091 35 K 0.0169 0.6185 0.3646 36 F 0.0474 0.2554 0.6972 37 I 0.0542 0.2325 0.7133 38 T 0.0389 0.3772 0.5839 39 K 0.0291 0.4879 0.4830 40 K 0.0497 0.4730 0.4773 41 L 0.0822 0.4639 0.4539 42 D 0.0949 0.4949 0.4102 43 W 0.1101 0.5387 0.3512 44 K 0.1161 0.5719 0.3120 45 I 0.1493 0.5195 0.3311 46 N 0.1766 0.5226 0.3008 47 L 0.1738 0.5127 0.3135 48 S 0.1244 0.4082 0.4674 49 S 0.1120 0.2303 0.6577 50 F 0.1268 0.2725 0.6007 51 P 0.0924 0.5101 0.3975 52 S 0.1485 0.5961 0.2554 53 Y 0.2769 0.5623 0.1608 54 I 0.3816 0.4800 0.1384 55 Y 0.4223 0.4296 0.1481 56 A 0.4057 0.4068 0.1875 57 K 0.3635 0.3648 0.2717 58 A 0.2903 0.2627 0.4470 59 E 0.1452 0.2480 0.6068 60 K 0.0849 0.1823 0.7328 61 H 0.1050 0.1735 0.7214 62 F 0.0912 0.2648 0.6440 63 D 0.0758 0.3778 0.5464 64 E 0.0776 0.4040 0.5184 65 L 0.0959 0.5188 0.3853 66 V 0.1256 0.6147 0.2597 67 E 0.1290 0.6584 0.2126 68 Y 0.0741 0.7712 0.1547 69 G 0.0457 0.8265 0.1278 70 F 0.0228 0.8877 0.0895 71 Q 0.0129 0.9206 0.0664 72 G 0.0122 0.9290 0.0589 73 E 0.0103 0.9398 0.0499 74 Q 0.0107 0.9382 0.0511 75 I 0.0070 0.9497 0.0433 76 V 0.0085 0.9486 0.0429 77 L 0.0080 0.9481 0.0438 78 F 0.0076 0.9445 0.0478 79 L 0.0068 0.9376 0.0556 80 T 0.0076 0.9087 0.0837 81 A 0.0129 0.7975 0.1896 82 Q 0.0471 0.4130 0.5399 83 G 0.0442 0.0806 0.8753 84 F 0.0956 0.0732 0.8312 85 G 0.2493 0.0779 0.6728 86 T 0.4074 0.1163 0.4763 87 C 0.4776 0.1259 0.3965 88 W 0.4807 0.1530 0.3663 89 M 0.4358 0.1406 0.4236 90 A 0.3347 0.1285 0.5368 91 R 0.2929 0.0968 0.6103 92 S 0.2325 0.1082 0.6593 93 P 0.1454 0.1323 0.7223 94 H 0.0956 0.1261 0.7783 95 P 0.0891 0.1618 0.7491 96 D 0.1210 0.1664 0.7126 97 V 0.2958 0.1255 0.5787 98 P 0.4475 0.0940 0.4585 99 Y 0.6041 0.0692 0.3267 100 I 0.6867 0.0640 0.2493 101 I 0.7936 0.0408 0.1656 102 V 0.8450 0.0289 0.1261 103 F 0.8143 0.0310 0.1547 104 G 0.7456 0.0301 0.2243 105 Y 0.5836 0.0268 0.3896 106 P 0.4212 0.0401 0.5387 107 R 0.1783 0.1090 0.7127 108 T 0.0844 0.1509 0.7647 109 R 0.0534 0.3192 0.6274 110 N 0.0627 0.3582 0.5791 111 F 0.0845 0.3729 0.5426 112 T 0.0987 0.3113 0.5900 113 R 0.1166 0.3858 0.4976 114 K 0.1030 0.4308 0.4661 115 R 0.1048 0.4143 0.4809 116 R 0.0919 0.4866 0.4215 117 P 0.0734 0.5456 0.3810 118 I 0.0587 0.6068 0.3345 119 T 0.0473 0.6434 0.3092 120 S 0.0454 0.6443 0.3103 121 F 0.0574 0.5978 0.3447 122 L 0.0540 0.5971 0.3489 123 E 0.0380 0.6036 0.3584 124 N 0.0405 0.5346 0.4249 125 D 0.0515 0.4047 0.5439 126 L 0.0338 0.5425 0.4237 127 E 0.0163 0.5801 0.4036 128 E 0.0246 0.4676 0.5078 129 L 0.0490 0.2964 0.6546 130 P 0.0494 0.2777 0.6729 131 P 0.0058 0.9097 0.0845 132 E 0.0053 0.9286 0.0662 133 I 0.0048 0.9513 0.0439 134 V 0.0047 0.9579 0.0374 135 K 0.0048 0.9556 0.0396 136 I 0.0048 0.9551 0.0401 137 V 0.0051 0.9560 0.0390 138 E 0.0050 0.9495 0.0455 139 M 0.0053 0.9398 0.0549 140 T 0.0067 0.9197 0.0736 141 I 0.0084 0.8263 0.1653 142 L 0.0150 0.6060 0.3790 143 A 0.0567 0.1340 0.8093 144 P 0.0582 0.1240 0.8178 145 S 0.0767 0.2066 0.7167 146 A 0.0876 0.3207 0.5917 147 L 0.0976 0.2769 0.6255 148 N 0.1298 0.1426 0.7276 149 R 0.1532 0.0669 0.7798 150 Q 0.1968 0.0223 0.7809 151 P 0.2670 0.0200 0.7130 152 W 0.5838 0.0117 0.4045 153 K 0.8544 0.0073 0.1383 154 I 0.9052 0.0048 0.0900 155 K 0.9086 0.0037 0.0877 156 Y 0.8807 0.0042 0.1151 157 T 0.6897 0.0133 0.2970 158 G 0.2808 0.0262 0.6930 159 G 0.0788 0.0516 0.8696 160 E 0.0310 0.5274 0.4416 161 L 0.0315 0.6935 0.2750 162 C 0.0384 0.6877 0.2739 163 I 0.0565 0.6330 0.3104 164 S 0.0714 0.6011 0.3275 165 S 0.0658 0.5549 0.3793 166 E 0.0813 0.4717 0.4470 167 R 0.1075 0.4206 0.4720 168 P 0.0770 0.5388 0.3842 169 V 0.1028 0.5449 0.3523 170 D 0.1116 0.5295 0.3589 171 L 0.0745 0.4378 0.4877 172 G 0.0709 0.1794 0.7497 173 I 0.1485 0.1099 0.7416 174 A 0.2666 0.1021 0.6313 175 L 0.5426 0.1339 0.3235 176 S 0.7189 0.1099 0.1712 177 H 0.8362 0.0610 0.1028 178 A 0.8623 0.0442 0.0935 179 Y 0.8300 0.0442 0.1258 180 L 0.5982 0.0810 0.3208 181 T 0.2543 0.1194 0.6263 182 A 0.1238 0.1867 0.6895 183 R 0.0515 0.3910 0.5575 184 E 0.0548 0.5005 0.4448 185 I 0.0473 0.6065 0.3462 186 F 0.0708 0.6279 0.3013 187 K 0.1086 0.6286 0.2628 188 R 0.1291 0.5924 0.2786 189 E 0.1406 0.5487 0.3108 190 P 0.1422 0.5027 0.3551 191 V 0.1510 0.4892 0.3598 192 I 0.1763 0.4411 0.3827 193 Q 0.2181 0.3441 0.4378 194 K 0.3006 0.2250 0.4744 195 R 0.2551 0.1519 0.5930 196 G 0.1697 0.1242 0.7061 197 E 0.0740 0.3504 0.5755 198 D 0.1034 0.3372 0.5594 199 T 0.2142 0.3555 0.4303 200 Y 0.3558 0.2834 0.3609 201 C 0.5319 0.2125 0.2557 202 L 0.6094 0.1816 0.2090 203 I 0.5525 0.1819 0.2655 204 L 0.3336 0.1228 0.5435 205 N 0.1178 0.0419 0.8402 206 P 0.0439 0.0363 0.9198