# This file is the result of combining several RDB files, specifically # T0350.t06.dssp-ebghstl.rdb (weight 1.53986) # T0350.t06.stride-ebghtl.rdb (weight 1.24869) # T0350.t06.str2.rdb (weight 1.54758) # T0350.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 T0350.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0350 # 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 T0350.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 127 # # ============================================ # Comments from T0350.t06.stride-ebghtl.rdb # ============================================ # TARGET T0350 # 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 T0350.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 127 # # ============================================ # Comments from T0350.t06.str2.rdb # ============================================ # TARGET T0350 # 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 T0350.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 127 # # ============================================ # Comments from T0350.t06.alpha.rdb # ============================================ # TARGET T0350 # 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 T0350.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 127 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0768 0.0157 0.9075 2 N 0.1342 0.0167 0.8491 3 I 0.1394 0.2121 0.6485 4 E 0.1584 0.2732 0.5684 5 R 0.1950 0.3528 0.4522 6 L 0.2301 0.2058 0.5641 7 T 0.2387 0.1753 0.5860 8 T 0.2057 0.2090 0.5853 9 L 0.1718 0.1871 0.6411 10 Q 0.1139 0.1415 0.7446 11 P 0.1111 0.1772 0.7117 12 V 0.1127 0.2836 0.6036 13 W 0.1173 0.2264 0.6564 14 D 0.0946 0.2399 0.6655 15 R 0.0659 0.3954 0.5387 16 Y 0.0873 0.3847 0.5280 17 D 0.0835 0.3717 0.5448 18 T 0.0641 0.5630 0.3729 19 Q 0.0981 0.5123 0.3896 20 I 0.1095 0.4836 0.4068 21 H 0.1374 0.3862 0.4763 22 N 0.1449 0.2934 0.5618 23 Q 0.0979 0.3171 0.5850 24 K 0.0882 0.2878 0.6240 25 D 0.0765 0.2190 0.7044 26 N 0.0579 0.2181 0.7240 27 D 0.0724 0.2107 0.7170 28 N 0.1021 0.1443 0.7536 29 E 0.1310 0.1065 0.7624 30 V 0.1335 0.0399 0.8265 31 P 0.1245 0.0556 0.8198 32 V 0.1324 0.1357 0.7319 33 H 0.1855 0.1273 0.6872 34 Q 0.2134 0.0943 0.6924 35 V 0.1972 0.0341 0.7688 36 S 0.0976 0.0216 0.8807 37 Y 0.0060 0.9202 0.0738 38 T 0.0051 0.9364 0.0585 39 N 0.0049 0.9390 0.0561 40 L 0.0047 0.9577 0.0376 41 A 0.0047 0.9600 0.0353 42 E 0.0047 0.9583 0.0370 43 M 0.0047 0.9561 0.0392 44 V 0.0047 0.9558 0.0395 45 G 0.0047 0.9533 0.0420 46 E 0.0048 0.9452 0.0500 47 M 0.0049 0.9330 0.0622 48 N 0.0058 0.8949 0.0993 49 K 0.0080 0.8296 0.1624 50 L 0.0142 0.7328 0.2530 51 L 0.0940 0.3422 0.5638 52 E 0.1291 0.0969 0.7740 53 P 0.1355 0.2153 0.6492 54 S 0.1598 0.1907 0.6495 55 Q 0.2528 0.1072 0.6400 56 V 0.5016 0.0382 0.4602 57 H 0.7687 0.0079 0.2235 58 L 0.8820 0.0037 0.1144 59 K 0.9109 0.0041 0.0850 60 F 0.9157 0.0035 0.0808 61 E 0.9080 0.0046 0.0874 62 L 0.8763 0.0068 0.1169 63 H 0.6417 0.0108 0.3475 64 D 0.0727 0.2415 0.6858 65 K 0.0498 0.2171 0.7331 66 L 0.0779 0.1261 0.7960 67 N 0.0829 0.0308 0.8863 68 E 0.3375 0.0091 0.6534 69 Y 0.8207 0.0038 0.1756 70 Y 0.8983 0.0039 0.0978 71 V 0.9208 0.0036 0.0755 72 K 0.9239 0.0038 0.0722 73 V 0.9230 0.0033 0.0736 74 I 0.8761 0.0060 0.1179 75 E 0.6622 0.0080 0.3298 76 D 0.0363 0.1352 0.8285 77 S 0.0254 0.1180 0.8566 78 T 0.0729 0.0775 0.8496 79 N 0.0675 0.0667 0.8658 80 E 0.4274 0.0739 0.4987 81 V 0.7863 0.0792 0.1345 82 I 0.7822 0.0762 0.1416 83 R 0.7561 0.0769 0.1670 84 E 0.6308 0.0591 0.3101 85 I 0.2571 0.0243 0.7187 86 P 0.0753 0.0131 0.9116 87 P 0.0186 0.7587 0.2227 88 K 0.0050 0.9370 0.0580 89 R 0.0051 0.9473 0.0476 90 W 0.0048 0.9575 0.0377 91 L 0.0047 0.9599 0.0355 92 D 0.0047 0.9600 0.0354 93 F 0.0048 0.9575 0.0378 94 Y 0.0048 0.9569 0.0383 95 A 0.0049 0.9475 0.0476 96 A 0.0053 0.9180 0.0768 97 M 0.0053 0.9075 0.0873 98 T 0.0064 0.8816 0.1120 99 E 0.0063 0.8669 0.1268 100 F 0.0108 0.8571 0.1321 101 L 0.0177 0.8047 0.1776 102 G 0.0272 0.7195 0.2533 103 L 0.0477 0.7471 0.2052 104 F 0.1089 0.6903 0.2008 105 V 0.1364 0.6000 0.2637 106 D 0.1334 0.4723 0.3942 107 E 0.0279 0.7690 0.2031 108 K 0.0374 0.7586 0.2040 109 K 0.0585 0.6959 0.2456 110 L 0.0773 0.5742 0.3485 111 E 0.0710 0.3887 0.5403 112 H 0.0365 0.4144 0.5491 113 H 0.0428 0.2697 0.6874 114 H 0.0731 0.1620 0.7648 115 H 0.0643 0.1495 0.7862 116 H 0.0742 0.0817 0.8441 117 H 0.0463 0.0427 0.9110