# This file is the result of combining several RDB files, specifically # T0406.t04.dssp-ebghstl.rdb (weight 1.53986) # T0406.t04.stride-ebghtl.rdb (weight 1.24869) # T0406.t04.str2.rdb (weight 1.54758) # T0406.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 T0406.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0406 # Using neural net t04-2621-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 T0406.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 771 # # ============================================ # Comments from T0406.t04.stride-ebghtl.rdb # ============================================ # TARGET T0406 # 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 T0406.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 771 # # ============================================ # Comments from T0406.t04.str2.rdb # ============================================ # TARGET T0406 # Using neural net t04-2621-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 T0406.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 771 # # ============================================ # Comments from T0406.t04.alpha.rdb # ============================================ # TARGET T0406 # 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 T0406.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 771 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0370 0.1474 0.8156 2 Y 0.0405 0.3780 0.5815 3 Q 0.0278 0.6345 0.3377 4 T 0.0147 0.8116 0.1737 5 I 0.0066 0.9330 0.0604 6 E 0.0053 0.9492 0.0455 7 G 0.0050 0.9545 0.0405 8 F 0.0050 0.9548 0.0402 9 L 0.0050 0.9536 0.0414 10 Q 0.0054 0.9462 0.0484 11 S 0.0059 0.9332 0.0609 12 W 0.0072 0.9145 0.0783 13 T 0.0065 0.8731 0.1204 14 Y 0.0098 0.8189 0.1713 15 E 0.0137 0.7480 0.2383 16 T 0.0071 0.8771 0.1158 17 E 0.0051 0.9110 0.0838 18 S 0.0065 0.9137 0.0798 19 T 0.0052 0.9371 0.0577 20 Q 0.0048 0.9532 0.0421 21 K 0.0048 0.9521 0.0432 22 M 0.0050 0.9414 0.0535 23 L 0.0065 0.8929 0.1006 24 D 0.0070 0.7034 0.2896 25 V 0.0181 0.3139 0.6681 26 L 0.0803 0.0253 0.8944 27 T 0.0571 0.0155 0.9275 28 D 0.0052 0.8912 0.1037 29 E 0.0058 0.9176 0.0766 30 S 0.0080 0.9120 0.0800 31 L 0.0241 0.8166 0.1592 32 S 0.0257 0.6170 0.3574 33 Q 0.0667 0.3446 0.5887 34 E 0.1056 0.1354 0.7591 35 I 0.1649 0.0891 0.7460 36 A 0.0709 0.0295 0.8996 37 P 0.0244 0.1017 0.8740 38 G 0.0239 0.0691 0.9070 39 H 0.0911 0.0946 0.8144 40 W 0.1369 0.0951 0.7680 41 T 0.1418 0.2571 0.6011 42 L 0.0054 0.9476 0.0470 43 G 0.0047 0.9601 0.0352 44 R 0.0047 0.9599 0.0355 45 V 0.0047 0.9599 0.0354 46 A 0.0047 0.9588 0.0365 47 W 0.0047 0.9569 0.0383 48 H 0.0048 0.9508 0.0445 49 I 0.0051 0.9483 0.0467 50 V 0.0064 0.9401 0.0536 51 T 0.0098 0.9129 0.0773 52 A 0.0112 0.9064 0.0824 53 I 0.0084 0.9336 0.0580 54 P 0.0067 0.9466 0.0467 55 V 0.0094 0.9403 0.0503 56 I 0.0111 0.9359 0.0529 57 L 0.0140 0.9173 0.0687 58 S 0.0099 0.8463 0.1438 59 G 0.0169 0.6754 0.3077 60 T 0.0641 0.3367 0.5992 61 G 0.0548 0.1027 0.8425 62 L 0.0784 0.0654 0.8562 63 K 0.0940 0.0977 0.8083 64 F 0.0976 0.0985 0.8040 65 E 0.0797 0.1066 0.8137 66 G 0.0771 0.1032 0.8197 67 E 0.1168 0.1139 0.7693 68 T 0.1350 0.1557 0.7093 69 K 0.0986 0.1542 0.7472 70 D 0.0872 0.1135 0.7993 71 Y 0.0862 0.0418 0.8720 72 P 0.0840 0.0430 0.8730 73 V 0.0749 0.0224 0.9026 74 P 0.0707 0.0196 0.9097 75 T 0.1071 0.0228 0.8701 76 S 0.0708 0.0334 0.8958 77 A 0.0048 0.9520 0.0432 78 K 0.0047 0.9606 0.0348 79 T 0.0047 0.9602 0.0351 80 I 0.0047 0.9601 0.0352 81 A 0.0047 0.9590 0.0363 82 D 0.0047 0.9561 0.0391 83 G 0.0047 0.9536 0.0416 84 Y 0.0048 0.9547 0.0405 85 R 0.0047 0.9578 0.0375 86 K 0.0048 0.9565 0.0388 87 V 0.0048 0.9545 0.0406 88 N 0.0048 0.9557 0.0395 89 T 0.0047 0.9600 0.0354 90 A 0.0047 0.9597 0.0356 91 F 0.0047 0.9598 0.0355 92 V 0.0047 0.9603 0.0351 93 E 0.0047 0.9594 0.0359 94 A 0.0049 0.9518 0.0433 95 L 0.0055 0.9133 0.0812 96 Q 0.0068 0.7369 0.2563 97 S 0.0293 0.3920 0.5787 98 E 0.0270 0.1690 0.8041 99 W 0.0837 0.0211 0.8953 100 T 0.0646 0.0190 0.9163 101 D 0.0059 0.8847 0.1094 102 K 0.0054 0.9045 0.0900 103 D 0.0083 0.8958 0.0959 104 L 0.0212 0.8262 0.1526 105 T 0.0311 0.7436 0.2253 106 T 0.0879 0.5807 0.3314 107 I 0.1550 0.3932 0.4518 108 N 0.2277 0.1734 0.5989 109 D 0.1511 0.1273 0.7215 110 F 0.1123 0.1296 0.7581 111 F 0.0682 0.0774 0.8543 112 G 0.0433 0.0476 0.9091 113 R 0.0941 0.0201 0.8857 114 P 0.1643 0.0164 0.8192 115 M 0.1579 0.0138 0.8283 116 P 0.0995 0.0232 0.8773 117 N 0.0053 0.9235 0.0712 118 S 0.0047 0.9572 0.0382 119 I 0.0047 0.9581 0.0372 120 F 0.0050 0.9597 0.0353 121 L 0.0047 0.9604 0.0350 122 M 0.0047 0.9605 0.0348 123 T 0.0047 0.9587 0.0366 124 L 0.0048 0.9536 0.0416 125 I 0.0058 0.9383 0.0559 126 N 0.0081 0.8881 0.1038 127 H 0.0110 0.8510 0.1380 128 Q 0.0093 0.8545 0.1361 129 N 0.0133 0.8147 0.1720 130 H 0.0164 0.7881 0.1955 131 H 0.0199 0.8310 0.1491 132 R 0.0059 0.9153 0.0788 133 G 0.0051 0.9447 0.0502 134 Q 0.0047 0.9595 0.0358 135 M 0.0047 0.9611 0.0342 136 T 0.0046 0.9617 0.0337 137 V 0.0046 0.9618 0.0336 138 L 0.0046 0.9615 0.0339 139 M 0.0047 0.9605 0.0348 140 R 0.0049 0.9547 0.0403 141 Q 0.0062 0.9273 0.0665 142 A 0.0451 0.4952 0.4596 143 G 0.0360 0.0300 0.9340 144 L 0.0746 0.0166 0.9088 145 T 0.1341 0.0194 0.8465 146 V 0.1400 0.0248 0.8352 147 P 0.1083 0.0844 0.8073 148 G 0.1015 0.1351 0.7634 149 V 0.1215 0.1129 0.7656 150 Y 0.1123 0.0893 0.7985 151 G 0.0873 0.0572 0.8555 152 P 0.0943 0.0976 0.8082 153 A 0.0889 0.1770 0.7340 154 K 0.0459 0.5080 0.4461 155 E 0.0162 0.8074 0.1764 156 E 0.0190 0.8184 0.1625 157 W 0.0259 0.8141 0.1600 158 A 0.0250 0.8099 0.1651 159 T 0.0271 0.7700 0.2029 160 A 0.0396 0.5832 0.3772 161 G 0.0393 0.3423 0.6184 162 M 0.0640 0.2617 0.6743 163 E 0.0858 0.2137 0.7005 164 A 0.0780 0.0857 0.8363 165 P 0.0390 0.1755 0.7855 166 K 0.0560 0.1370 0.8070 167 M 0.0561 0.0521 0.8918