# This file is the result of combining several RDB files, specifically # T0304.t06.dssp-ebghstl.rdb (weight 1.53986) # T0304.t06.stride-ebghtl.rdb (weight 1.24869) # T0304.t06.str2.rdb (weight 1.54758) # T0304.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 T0304.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0304 # 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 T0304.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 4.63225 # # ============================================ # Comments from T0304.t06.stride-ebghtl.rdb # ============================================ # TARGET T0304 # 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 T0304.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 4.63225 # # ============================================ # Comments from T0304.t06.str2.rdb # ============================================ # TARGET T0304 # 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 T0304.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 4.63225 # # ============================================ # Comments from T0304.t06.alpha.rdb # ============================================ # TARGET T0304 # 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 T0304.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 4.63225 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0810 0.0577 0.8613 2 S 0.1248 0.1255 0.7498 3 D 0.1459 0.1608 0.6933 4 T 0.1643 0.1363 0.6994 5 L 0.1465 0.0579 0.7955 6 P 0.0592 0.1028 0.8380 7 G 0.0667 0.0839 0.8494 8 T 0.2488 0.0558 0.6954 9 T 0.3636 0.0349 0.6016 10 L 0.2126 0.0224 0.7650 11 P 0.1155 0.0455 0.8390 12 D 0.0615 0.1499 0.7885 13 D 0.0597 0.1830 0.7573 14 N 0.0686 0.1776 0.7538 15 H 0.0989 0.1161 0.7850 16 D 0.1170 0.0923 0.7908 17 R 0.1236 0.0564 0.8200 18 P 0.1245 0.1568 0.7187 19 W 0.2131 0.2286 0.5583 20 W 0.2688 0.1717 0.5595 21 G 0.2171 0.0824 0.7005 22 L 0.2590 0.0301 0.7109 23 P 0.2680 0.0435 0.6885 24 C 0.2978 0.0595 0.6427 25 T 0.3388 0.0551 0.6061 26 V 0.4254 0.0457 0.5290 27 T 0.2885 0.0460 0.6655 28 P 0.1732 0.1793 0.6474 29 C 0.1966 0.2197 0.5837 30 F 0.2418 0.2808 0.4774 31 G 0.2620 0.2361 0.5018 32 A 0.3800 0.2737 0.3464 33 R 0.4431 0.3601 0.1968 34 L 0.5316 0.3506 0.1178 35 V 0.5073 0.3461 0.1467 36 Q 0.4323 0.3456 0.2221 37 E 0.2091 0.2933 0.4976 38 G 0.0696 0.1101 0.8204 39 N 0.0833 0.1474 0.7692 40 R 0.2870 0.2426 0.4704 41 L 0.4614 0.2435 0.2951 42 H 0.4576 0.2651 0.2773 43 Y 0.5422 0.2734 0.1844 44 L 0.4453 0.3358 0.2189 45 A 0.3104 0.3858 0.3039 46 D 0.3052 0.3631 0.3317 47 R 0.2840 0.3620 0.3541 48 A 0.3543 0.1829 0.4628 49 G 0.4308 0.0986 0.4706 50 I 0.6573 0.0483 0.2944 51 R 0.6344 0.0628 0.3028 52 G 0.6322 0.0252 0.3426 53 L 0.5951 0.0230 0.3819 54 F 0.3554 0.0230 0.6216 55 S 0.1372 0.0315 0.8314 56 D 0.0295 0.5715 0.3989 57 A 0.0165 0.7337 0.2498 58 D 0.0277 0.7381 0.2342 59 A 0.0571 0.7322 0.2107 60 Y 0.0480 0.7362 0.2157 61 H 0.0470 0.7280 0.2250 62 L 0.0111 0.8595 0.1294 63 D 0.0080 0.8966 0.0954 64 Q 0.0062 0.8899 0.1039 65 A 0.0072 0.8733 0.1195 66 F 0.0054 0.8929 0.1017 67 P 0.0047 0.9522 0.0431 68 L 0.0047 0.9577 0.0376 69 L 0.0047 0.9584 0.0370 70 M 0.0047 0.9594 0.0359 71 K 0.0047 0.9573 0.0379 72 Q 0.0050 0.9518 0.0432 73 L 0.0050 0.9472 0.0478 74 E 0.0053 0.9437 0.0510 75 L 0.0061 0.9295 0.0645 76 M 0.0075 0.8976 0.0949 77 L 0.0275 0.7745 0.1979 78 T 0.0449 0.5578 0.3973 79 S 0.0620 0.3269 0.6111 80 G 0.0595 0.1652 0.7753 81 E 0.1699 0.1170 0.7131 82 L 0.3118 0.0549 0.6333 83 N 0.1387 0.0138 0.8475 84 P 0.0284 0.2585 0.7131 85 R 0.0366 0.2562 0.7072 86 H 0.1133 0.2222 0.6645 87 Q 0.2287 0.0784 0.6930 88 H 0.4401 0.0390 0.5208 89 T 0.7897 0.0137 0.1967 90 V 0.8825 0.0073 0.1101 91 T 0.8932 0.0104 0.0965 92 L 0.8536 0.0218 0.1246 93 Y 0.7243 0.0311 0.2446 94 A 0.4720 0.0752 0.4528 95 K 0.1245 0.0900 0.7855 96 G 0.1356 0.0451 0.8193 97 L 0.4117 0.0242 0.5641 98 T 0.6456 0.0267 0.3278 99 C 0.6402 0.0455 0.3143 100 K 0.5492 0.0844 0.3664 101 A 0.4308 0.1093 0.4599 102 D 0.3974 0.1146 0.4881 103 T 0.4217 0.0976 0.4807 104 L 0.2890 0.1356 0.5753 105 S 0.1807 0.1216 0.6977 106 S 0.1918 0.1112 0.6970 107 C 0.1855 0.1050 0.7095 108 D 0.2867 0.0579 0.6554 109 Y 0.7338 0.0128 0.2534 110 V 0.9108 0.0045 0.0847 111 Y 0.9276 0.0049 0.0675 112 L 0.9273 0.0054 0.0673 113 A 0.9200 0.0061 0.0739 114 V 0.8851 0.0119 0.1030 115 Y 0.7345 0.0083 0.2573 116 P 0.3702 0.0238 0.6060 117 T 0.1309 0.0234 0.8458 118 P 0.0380 0.2962 0.6658 119 E 0.0478 0.3187 0.6335 120 M 0.0895 0.2406 0.6698 121 K 0.0666 0.1228 0.8107 122 N 0.0463 0.0360 0.9177