# This file is the result of combining several RDB files, specifically # T0308.t04.dssp-ebghstl.rdb (weight 1.53986) # T0308.t04.stride-ebghtl.rdb (weight 1.24869) # T0308.t04.str2.rdb (weight 1.54758) # T0308.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 T0308.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0308 # 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 T0308.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 40.9228 # # ============================================ # Comments from T0308.t04.stride-ebghtl.rdb # ============================================ # TARGET T0308 # 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 T0308.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 40.9228 # # ============================================ # Comments from T0308.t04.str2.rdb # ============================================ # TARGET T0308 # 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 T0308.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 40.9228 # # ============================================ # Comments from T0308.t04.alpha.rdb # ============================================ # TARGET T0308 # 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 T0308.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 40.9228 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 E 0.1279 0.0188 0.8533 2 V 0.4878 0.0057 0.5065 3 H 0.8111 0.0047 0.1842 4 V 0.9316 0.0032 0.0651 5 L 0.9325 0.0033 0.0642 6 C 0.9307 0.0032 0.0661 7 L 0.8558 0.0203 0.1239 8 G 0.5319 0.0102 0.4579 9 L 0.1650 0.0632 0.7718 10 D 0.0478 0.1430 0.8092 11 N 0.0336 0.1720 0.7944 12 S 0.0801 0.1453 0.7746 13 G 0.0961 0.1257 0.7783 14 K 0.1460 0.5875 0.2664 15 T 0.2298 0.5841 0.1861 16 T 0.2471 0.5991 0.1538 17 I 0.2030 0.6879 0.1091 18 I 0.1818 0.7006 0.1176 19 N 0.1942 0.6405 0.1653 20 K 0.2334 0.4862 0.2804 21 L 0.2809 0.2692 0.4499 22 K 0.1177 0.0442 0.8381 23 P 0.0559 0.1640 0.7801 24 S 0.0330 0.1764 0.7906 25 N 0.0703 0.1589 0.7708 26 A 0.1685 0.1505 0.6809 27 Q 0.3131 0.1130 0.5739 28 S 0.2482 0.1120 0.6398 29 Q 0.1641 0.1643 0.6716 30 N 0.2378 0.0957 0.6665 31 I 0.4346 0.0554 0.5100 32 L 0.3841 0.0390 0.5769 33 P 0.3556 0.0577 0.5868 34 T 0.3942 0.0620 0.5437 35 I 0.3849 0.0814 0.5337 36 G 0.3035 0.0452 0.6513 37 F 0.3737 0.0210 0.6053 38 S 0.6193 0.0083 0.3724 39 I 0.7780 0.0075 0.2145 40 E 0.8539 0.0068 0.1394 41 K 0.9077 0.0038 0.0884 42 F 0.8920 0.0050 0.1030 43 K 0.8708 0.0062 0.1230 44 S 0.6470 0.0288 0.3242 45 S 0.0744 0.0728 0.8527 46 S 0.1034 0.0338 0.8628 47 L 0.6478 0.0068 0.3454 48 S 0.8613 0.0082 0.1305 49 F 0.9194 0.0035 0.0771 50 T 0.9209 0.0036 0.0755 51 V 0.9149 0.0039 0.0812 52 F 0.8585 0.0098 0.1316 53 D 0.6028 0.0293 0.3679 54 M 0.2055 0.1200 0.6745 55 S 0.1027 0.1573 0.7400 56 G 0.0724 0.1824 0.7452 57 Q 0.0709 0.3776 0.5515 58 G 0.0497 0.5451 0.4052 59 R 0.0464 0.5874 0.3661 60 Y 0.0517 0.6304 0.3179 61 R 0.0345 0.6945 0.2710 62 N 0.0376 0.7033 0.2591 63 L 0.0237 0.7815 0.1948 64 W 0.0236 0.8024 0.1740 65 E 0.0127 0.8666 0.1207 66 H 0.0169 0.8512 0.1319 67 Y 0.0314 0.8021 0.1665 68 Y 0.0644 0.6451 0.2905 69 K 0.0369 0.4689 0.4943 70 E 0.0553 0.1710 0.7737 71 G 0.1620 0.0218 0.8163 72 Q 0.1741 0.0416 0.7843 73 A 0.9003 0.0038 0.0958 74 I 0.9286 0.0032 0.0682 75 I 0.9342 0.0031 0.0626 76 F 0.9316 0.0033 0.0651 77 V 0.9212 0.0035 0.0752 78 I 0.8628 0.0073 0.1299 79 D 0.5458 0.0078 0.4465 80 S 0.0872 0.1594 0.7534 81 S 0.0525 0.1628 0.7848 82 D 0.0715 0.2156 0.7129 83 R 0.0243 0.6813 0.2944 84 L 0.0292 0.7372 0.2336 85 R 0.0359 0.8145 0.1496 86 M 0.0117 0.9235 0.0649 87 V 0.0078 0.9439 0.0483 88 V 0.0073 0.9478 0.0449 89 A 0.0051 0.9519 0.0430 90 K 0.0051 0.9561 0.0387 91 E 0.0048 0.9569 0.0383 92 E 0.0049 0.9538 0.0413 93 L 0.0048 0.9542 0.0409 94 D 0.0048 0.9546 0.0406 95 T 0.0051 0.9484 0.0465 96 L 0.0059 0.9248 0.0693 97 L 0.0085 0.8333 0.1582 98 N 0.0159 0.4431 0.5410 99 H 0.0719 0.0541 0.8740 100 P 0.0151 0.2794 0.7056 101 D 0.0402 0.2958 0.6640 102 I 0.0861 0.4117 0.5022 103 K 0.0681 0.3394 0.5925 104 H 0.0460 0.2958 0.6582 105 R 0.0402 0.1673 0.7926 106 R 0.0757 0.0682 0.8561 107 I 0.1703 0.0123 0.8173 108 P 0.3736 0.0053 0.6211 109 I 0.9234 0.0036 0.0730 110 L 0.9321 0.0033 0.0646 111 F 0.9335 0.0032 0.0633 112 F 0.9143 0.0043 0.0814 113 A 0.7529 0.0088 0.2383 114 N 0.4409 0.0222 0.5370 115 K 0.1769 0.1781 0.6450 116 M 0.1163 0.2547 0.6290 117 D 0.0987 0.2197 0.6815 118 L 0.0342 0.5486 0.4172 119 R 0.0218 0.6198 0.3583 120 D 0.0330 0.5231 0.4439 121 A 0.0538 0.4764 0.4699 122 V 0.1175 0.2598 0.6226 123 T 0.1021 0.1961 0.7018 124 S 0.0442 0.6811 0.2747 125 V 0.0558 0.7570 0.1872 126 K 0.0667 0.7841 0.1492 127 V 0.0759 0.7656 0.1585 128 S 0.0539 0.7644 0.1817 129 Q 0.0153 0.9149 0.0698 130 L 0.0113 0.9245 0.0642 131 L 0.0102 0.9138 0.0759 132 C 0.0139 0.9025 0.0835 133 L 0.0108 0.9082 0.0811 134 E 0.0093 0.8878 0.1029 135 N 0.0088 0.8550 0.1361 136 I 0.0210 0.7623 0.2166 137 K 0.0142 0.5932 0.3925 138 D 0.0217 0.2828 0.6954 139 K 0.0667 0.0360 0.8973 140 P 0.0818 0.0428 0.8754 141 W 0.3205 0.0206 0.6588 142 H 0.7509 0.0143 0.2348 143 I 0.8837 0.0080 0.1083 144 C 0.8605 0.0098 0.1297 145 A 0.8003 0.0111 0.1886 146 S 0.6168 0.0296 0.3537 147 D 0.4626 0.0529 0.4845 148 A 0.1703 0.2300 0.5997 149 I 0.0963 0.2623 0.6414 150 K 0.0781 0.1862 0.7357 151 G 0.0446 0.1234 0.8320 152 E 0.0695 0.2252 0.7053 153 G 0.1213 0.3071 0.5716 154 L 0.0254 0.7991 0.1755 155 Q 0.0095 0.9217 0.0688 156 E 0.0081 0.9394 0.0526 157 G 0.0056 0.9480 0.0464 158 V 0.0047 0.9573 0.0381 159 D 0.0047 0.9608 0.0346 160 W 0.0047 0.9588 0.0366 161 L 0.0048 0.9522 0.0430 162 Q 0.0049 0.9368 0.0583 163 D 0.0054 0.8615 0.1331 164 Q 0.0085 0.6720 0.3194 165 I 0.0259 0.1276 0.8465