# This file is the result of combining several RDB files, specifically # T0352.t06.dssp-ebghstl.rdb (weight 1.53986) # T0352.t06.stride-ebghtl.rdb (weight 1.24869) # T0352.t06.str2.rdb (weight 1.54758) # T0352.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 T0352.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0352 # 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 T0352.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 18.4613 # # ============================================ # Comments from T0352.t06.stride-ebghtl.rdb # ============================================ # TARGET T0352 # 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 T0352.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 18.4613 # # ============================================ # Comments from T0352.t06.str2.rdb # ============================================ # TARGET T0352 # 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 T0352.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 18.4613 # # ============================================ # Comments from T0352.t06.alpha.rdb # ============================================ # TARGET T0352 # 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 T0352.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 18.4613 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0599 0.0243 0.9159 2 T 0.0666 0.0851 0.8483 3 T 0.0411 0.3937 0.5652 4 H 0.0188 0.6692 0.3120 5 D 0.0061 0.9009 0.0930 6 R 0.0059 0.9330 0.0611 7 V 0.0047 0.9527 0.0426 8 R 0.0047 0.9584 0.0370 9 L 0.0047 0.9554 0.0399 10 Q 0.0047 0.9529 0.0424 11 L 0.0047 0.9599 0.0355 12 Q 0.0046 0.9614 0.0340 13 A 0.0046 0.9604 0.0349 14 L 0.0047 0.9587 0.0366 15 E 0.0047 0.9605 0.0348 16 A 0.0047 0.9592 0.0361 17 L 0.0047 0.9551 0.0402 18 L 0.0047 0.9486 0.0466 19 R 0.0049 0.9126 0.0825 20 E 0.0064 0.8412 0.1524 21 H 0.0446 0.5828 0.3726 22 Q 0.0297 0.2863 0.6840 23 H 0.0522 0.3279 0.6199 24 W 0.1271 0.3291 0.5438 25 R 0.1304 0.2518 0.6178 26 N 0.1121 0.1502 0.7377 27 D 0.0837 0.0576 0.8586 28 E 0.0723 0.0266 0.9011 29 P 0.0796 0.0204 0.9000 30 Q 0.0769 0.0306 0.8925 31 P 0.0100 0.7722 0.2178 32 H 0.0089 0.8036 0.1875 33 Q 0.0128 0.8077 0.1795 34 F 0.0783 0.5204 0.4012 35 N 0.0548 0.2502 0.6950 36 S 0.0928 0.1194 0.7878 37 T 0.0607 0.1065 0.8329 38 Q 0.0770 0.0403 0.8827 39 P 0.1208 0.0859 0.7932 40 F 0.3422 0.1243 0.5334 41 F 0.4780 0.1482 0.3739 42 M 0.4591 0.1675 0.3734 43 D 0.3454 0.1603 0.4944 44 T 0.1800 0.1345 0.6854 45 M 0.1232 0.1265 0.7503 46 E 0.0806 0.1954 0.7239 47 P 0.0098 0.8309 0.1593 48 L 0.0099 0.8659 0.1242 49 E 0.0131 0.9043 0.0826 50 W 0.0168 0.9199 0.0633 51 L 0.0122 0.9240 0.0638 52 Q 0.0160 0.9291 0.0550 53 W 0.0133 0.9342 0.0525 54 V 0.0215 0.8897 0.0887 55 L 0.0189 0.8651 0.1160 56 I 0.0267 0.8369 0.1363 57 P 0.0148 0.8309 0.1544 58 R 0.0159 0.8195 0.1647 59 M 0.0049 0.9385 0.0566 60 H 0.0048 0.9478 0.0473 61 D 0.0049 0.9510 0.0441 62 L 0.0053 0.9453 0.0494 63 L 0.0061 0.9252 0.0687 64 D 0.0095 0.8153 0.1752 65 N 0.0456 0.4196 0.5348 66 K 0.0302 0.1360 0.8337 67 Q 0.0570 0.0222 0.9209 68 P 0.0990 0.0331 0.8679 69 L 0.0826 0.0284 0.8890 70 P 0.0508 0.1238 0.8254 71 G 0.0260 0.2271 0.7470 72 A 0.0656 0.3627 0.5717 73 F 0.1537 0.3034 0.5429 74 A 0.2661 0.2786 0.4553 75 V 0.1914 0.4171 0.3915 76 A 0.0605 0.7031 0.2364 77 P 0.0302 0.8416 0.1282 78 Y 0.0183 0.9120 0.0696 79 Y 0.0140 0.9347 0.0513 80 E 0.0124 0.9409 0.0467 81 M 0.0091 0.9411 0.0498 82 A 0.0081 0.9303 0.0616 83 L 0.0112 0.8822 0.1066 84 A 0.0161 0.7612 0.2227 85 T 0.0226 0.4951 0.4823 86 D 0.0331 0.2436 0.7233 87 H 0.0452 0.2158 0.7389 88 P 0.0188 0.4694 0.5118 89 Q 0.0173 0.7010 0.2818 90 R 0.0113 0.8643 0.1244 91 A 0.0074 0.9255 0.0671 92 L 0.0082 0.9369 0.0548 93 I 0.0066 0.9462 0.0473 94 L 0.0051 0.9534 0.0415 95 A 0.0050 0.9551 0.0399 96 E 0.0048 0.9551 0.0401 97 L 0.0047 0.9557 0.0395 98 E 0.0048 0.9565 0.0388 99 K 0.0048 0.9501 0.0450 100 L 0.0048 0.9490 0.0462 101 D 0.0048 0.9483 0.0469 102 A 0.0053 0.9356 0.0591 103 L 0.0064 0.8922 0.1014 104 F 0.0154 0.7217 0.2629 105 A 0.0258 0.4607 0.5136 106 D 0.0401 0.3086 0.6513 107 D 0.0360 0.4076 0.5564 108 A 0.0328 0.5436 0.4236 109 S 0.0539 0.5881 0.3580 110 L 0.0699 0.6223 0.3078 111 E 0.0761 0.5491 0.3748 112 H 0.0774 0.4890 0.4337 113 H 0.0761 0.3928 0.5312 114 H 0.0849 0.2925 0.6226 115 H 0.0842 0.2125 0.7033 116 H 0.0709 0.1285 0.8005 117 H 0.0481 0.0399 0.9120