# This file is the result of combining several RDB files, specifically # T0263.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0263.t2k.stride-ebghtl.rdb (weight 1.24869) # T0263.t2k.str2.rdb (weight 1.54758) # T0263.t2k.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 T0263.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0263 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0263.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17 # # ============================================ # Comments from T0263.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0263 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0263.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17 # # ============================================ # Comments from T0263.t2k.str2.rdb # ============================================ # TARGET T0263 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0263.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17 # # ============================================ # Comments from T0263.t2k.alpha.rdb # ============================================ # TARGET T0263 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0263.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 17 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1087 0.0203 0.8710 2 A 0.2903 0.0227 0.6870 3 T 0.7805 0.0054 0.2141 4 L 0.8922 0.0047 0.1031 5 L 0.9150 0.0039 0.0812 6 Q 0.9181 0.0039 0.0780 7 L 0.8891 0.0057 0.1052 8 H 0.8402 0.0061 0.1536 9 F 0.6089 0.0101 0.3811 10 A 0.3866 0.0283 0.5851 11 F 0.1750 0.0467 0.7783 12 N 0.0829 0.0560 0.8612 13 G 0.0702 0.0490 0.8808 14 P 0.0621 0.1075 0.8305 15 F 0.0482 0.1811 0.7707 16 G 0.0335 0.3218 0.6446 17 D 0.0093 0.9180 0.0727 18 A 0.0060 0.9401 0.0539 19 M 0.0049 0.9494 0.0456 20 A 0.0050 0.9543 0.0408 21 E 0.0051 0.9475 0.0474 22 Q 0.0052 0.9390 0.0558 23 L 0.0051 0.9331 0.0618 24 K 0.0050 0.9357 0.0593 25 P 0.0050 0.9208 0.0742 26 L 0.0052 0.8930 0.1018 27 A 0.0066 0.8741 0.1193 28 E 0.0051 0.8754 0.1196 29 S 0.0056 0.8743 0.1201 30 I 0.0112 0.8368 0.1521 31 N 0.0126 0.7197 0.2677 32 Q 0.0218 0.5645 0.4137 33 E 0.0634 0.1888 0.7479 34 P 0.0425 0.1300 0.8275 35 G 0.0577 0.0737 0.8686 36 F 0.4126 0.0543 0.5332 37 L 0.7624 0.0183 0.2192 38 W 0.8456 0.0117 0.1428 39 K 0.8759 0.0068 0.1172 40 V 0.8903 0.0048 0.1049 41 W 0.8936 0.0053 0.1011 42 T 0.8713 0.0071 0.1216 43 E 0.7890 0.0129 0.1981 44 S 0.3025 0.0151 0.6824 45 E 0.0180 0.1253 0.8568 46 K 0.0282 0.0659 0.9059 47 N 0.0855 0.0549 0.8596 48 H 0.1863 0.0418 0.7719 49 E 0.5981 0.0292 0.3727 50 A 0.6063 0.0199 0.3738 51 G 0.5540 0.0192 0.4269 52 G 0.6998 0.0172 0.2830 53 I 0.8562 0.0118 0.1320 54 Y 0.8982 0.0082 0.0936 55 L 0.8744 0.0128 0.1128 56 F 0.7395 0.0226 0.2378 57 T 0.3807 0.0599 0.5594 58 D 0.2154 0.0460 0.7386 59 E 0.0072 0.8900 0.1028 60 K 0.0053 0.9278 0.0670 61 S 0.0050 0.9354 0.0596 62 A 0.0048 0.9454 0.0498 63 L 0.0048 0.9431 0.0521 64 A 0.0050 0.9126 0.0823 65 Y 0.0055 0.8899 0.1046 66 L 0.0059 0.9012 0.0929 67 E 0.0054 0.9141 0.0805 68 K 0.0056 0.9191 0.0753 69 H 0.0064 0.9297 0.0639 70 T 0.0060 0.9383 0.0558 71 A 0.0057 0.9395 0.0548 72 R 0.0059 0.9325 0.0617 73 L 0.0064 0.9258 0.0678 74 K 0.0080 0.8933 0.0987 75 N 0.0182 0.7290 0.2528 76 L 0.0552 0.3824 0.5624 77 G 0.0894 0.1417 0.7689 78 V 0.1270 0.0774 0.7956 79 E 0.1606 0.0878 0.7516 80 E 0.3377 0.0551 0.6072 81 V 0.6091 0.0299 0.3610 82 V 0.8517 0.0187 0.1295 83 A 0.8951 0.0106 0.0943 84 K 0.8727 0.0178 0.1095 85 V 0.8591 0.0243 0.1166 86 F 0.7608 0.0440 0.1953 87 D 0.6246 0.0557 0.3197 88 V 0.4300 0.1022 0.4678 89 N 0.2948 0.1884 0.5168 90 E 0.2702 0.2161 0.5137 91 P 0.3296 0.2702 0.4002 92 L 0.3030 0.3445 0.3525 93 S 0.2614 0.3568 0.3817 94 Q 0.2462 0.3772 0.3767 95 I 0.2087 0.3297 0.4616 96 N 0.1541 0.1898 0.6561 97 Q 0.1519 0.1114 0.7367 98 A 0.2000 0.0701 0.7299 99 K 0.2818 0.0559 0.6623 100 L 0.1334 0.0430 0.8237 101 A 0.0508 0.0252 0.9240