# This file is the result of combining several RDB files, specifically # T0222.t04.dssp-ebghstl.rdb (weight 1.53986) # T0222.t04.stride-ebghtl.rdb (weight 1.24869) # T0222.t04.str2.rdb (weight 1.54758) # T0222.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 T0222.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0222 # 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 T0222.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 27.9382 # # ============================================ # Comments from T0222.t04.stride-ebghtl.rdb # ============================================ # TARGET T0222 # 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 T0222.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 27.9382 # # ============================================ # Comments from T0222.t04.str2.rdb # ============================================ # TARGET T0222 # 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 T0222.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 27.9382 # # ============================================ # Comments from T0222.t04.alpha.rdb # ============================================ # TARGET T0222 # 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 T0222.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 27.9382 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 H 0.1932 0.0244 0.7825 2 F 0.4706 0.0178 0.5116 3 T 0.6324 0.0190 0.3486 4 I 0.5243 0.0713 0.4044 5 D 0.3319 0.0964 0.5717 6 K 0.0906 0.1495 0.7599 7 N 0.0896 0.0600 0.8504 8 L 0.0988 0.0335 0.8677 9 P 0.0776 0.0534 0.8690 10 G 0.0801 0.0593 0.8606 11 A 0.1132 0.1045 0.7823 12 D 0.1398 0.1388 0.7215 13 H 0.1396 0.2500 0.6105 14 S 0.1499 0.3323 0.5178 15 F 0.2448 0.2493 0.5059 16 A 0.3216 0.1069 0.5715 17 L 0.2728 0.0434 0.6838 18 N 0.1099 0.0136 0.8766 19 P 0.0053 0.8300 0.1647 20 D 0.0048 0.8893 0.1058 21 E 0.0055 0.9232 0.0713 22 L 0.0047 0.9525 0.0428 23 K 0.0047 0.9585 0.0368 24 E 0.0047 0.9542 0.0411 25 M 0.0048 0.9522 0.0430 26 V 0.0047 0.9523 0.0429 27 D 0.0047 0.9508 0.0445 28 G 0.0047 0.9443 0.0510 29 I 0.0047 0.9530 0.0423 30 R 0.0047 0.9559 0.0394 31 K 0.0047 0.9572 0.0382 32 T 0.0047 0.9568 0.0386 33 E 0.0047 0.9562 0.0391 34 A 0.0048 0.9496 0.0456 35 E 0.0058 0.9257 0.0686 36 L 0.0372 0.7371 0.2257 37 K 0.0242 0.3688 0.6070 38 Q 0.0505 0.2251 0.7245 39 G 0.0557 0.2240 0.7203 40 I 0.1009 0.2019 0.6972 41 T 0.0994 0.2435 0.6570 42 K 0.0758 0.4721 0.4521 43 P 0.0797 0.6049 0.3154 44 V 0.0862 0.6816 0.2323 45 S 0.0863 0.7053 0.2084 46 E 0.0649 0.7590 0.1761 47 K 0.0690 0.7141 0.2169 48 L 0.1020 0.6224 0.2756 49 L 0.1236 0.4307 0.4456 50 G 0.0853 0.1909 0.7239 51 S 0.0893 0.1213 0.7894 52 S 0.0927 0.1095 0.7977 53 Y 0.2562 0.0862 0.6577 54 K 0.3394 0.0689 0.5917 55 T 0.3329 0.0477 0.6194 56 T 0.2099 0.0589 0.7312 57 T 0.1416 0.0916 0.7669 58 A 0.0568 0.5887 0.3546 59 I 0.0596 0.6470 0.2934 60 E 0.0715 0.7132 0.2153 61 G 0.0586 0.7458 0.1956 62 E 0.0630 0.7573 0.1797 63 I 0.0574 0.7898 0.1528 64 R 0.0571 0.7921 0.1508 65 N 0.0689 0.7294 0.2016 66 F 0.1087 0.6163 0.2750 67 A 0.2239 0.4487 0.3274 68 Y 0.2788 0.3128 0.4084 69 R 0.4114 0.2630 0.3256 70 G 0.6003 0.1160 0.2837 71 I 0.8141 0.0527 0.1332 72 F 0.8553 0.0362 0.1085 73 T 0.8111 0.0322 0.1567 74 T 0.6054 0.0553 0.3393 75 A 0.4249 0.0362 0.5388 76 P 0.3960 0.0528 0.5511 77 I 0.1587 0.1039 0.7374 78 Q 0.1048 0.1193 0.7759 79 K 0.0420 0.1494 0.8086 80 G 0.0475 0.0845 0.8680 81 E 0.2739 0.0582 0.6678 82 A 0.6876 0.0202 0.2922 83 F 0.6258 0.0127 0.3614 84 S 0.3522 0.0168 0.6310 85 E 0.0496 0.6835 0.2669 86 D 0.0563 0.5467 0.3970 87 N 0.1230 0.4574 0.4197 88 I 0.6345 0.0919 0.2736 89 A 0.7979 0.0535 0.1486 90 V 0.8616 0.0222 0.1161 91 L 0.7715 0.0188 0.2096 92 R 0.4549 0.0128 0.5323 93 P 0.1297 0.0955 0.7748 94 G 0.0728 0.0669 0.8603 95 Q 0.1143 0.0659 0.8197 96 K 0.1069 0.0531 0.8400 97 P 0.0798 0.1348 0.7854 98 Q 0.0694 0.1222 0.8084 99 G 0.0823 0.0740 0.8437 100 L 0.1363 0.0289 0.8348 101 H 0.0910 0.0173 0.8917 102 P 0.0174 0.8018 0.1809 103 R 0.0129 0.8722 0.1149 104 F 0.0119 0.8854 0.1027 105 F 0.0087 0.9249 0.0664 106 E 0.0122 0.9052 0.0826 107 L 0.0253 0.8671 0.1076 108 L 0.0414 0.8078 0.1507 109 T 0.0535 0.6684 0.2780 110 S 0.0608 0.3626 0.5766 111 G 0.0743 0.1714 0.7544 112 V 0.3642 0.1390 0.4968 113 R 0.7050 0.0778 0.2172 114 A 0.6904 0.0804 0.2291 115 V 0.6736 0.0784 0.2480 116 R 0.5981 0.0640 0.3380 117 D 0.4760 0.0389 0.4851 118 I 0.2892 0.0176 0.6932 119 P 0.1312 0.0290 0.8398 120 A 0.0289 0.1167 0.8544 121 D 0.0271 0.0774 0.8956 122 T 0.1140 0.0549 0.8311 123 G 0.3301 0.0331 0.6368 124 I 0.5265 0.0207 0.4528 125 V 0.4397 0.0299 0.5304 126 W 0.1037 0.6523 0.2439 127 D 0.0474 0.7251 0.2275 128 D 0.0420 0.7638 0.1941 129 I 0.0901 0.7028 0.2071 130 L 0.1086 0.5789 0.3125 131 L 0.1165 0.4055 0.4780 132 K 0.0775 0.2075 0.7150 133 D 0.0790 0.0840 0.8369 134 S 0.0885 0.0532 0.8583 135 P 0.0976 0.0863 0.8161 136 F 0.1223 0.0971 0.7806 137 H 0.1092 0.0616 0.8291 138 E 0.0831 0.0503 0.8666