# This file is the result of combining several RDB files, specifically # T0306.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0306.t2k.stride-ebghtl.rdb (weight 1.24869) # T0306.t2k.str2.rdb (weight 1.54758) # T0306.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 T0306.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0306 # 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 T0306.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 78 # # ============================================ # Comments from T0306.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0306 # 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 T0306.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 78 # # ============================================ # Comments from T0306.t2k.str2.rdb # ============================================ # TARGET T0306 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0306.t2k-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 16.8416 # # ============================================ # Comments from T0306.t2k.alpha.rdb # ============================================ # TARGET T0306 # 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 T0306.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 78 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1166 0.0228 0.8607 2 K 0.4433 0.0376 0.5191 3 L 0.6997 0.0241 0.2762 4 A 0.7796 0.0191 0.2013 5 V 0.8504 0.0118 0.1378 6 V 0.7530 0.0230 0.2240 7 T 0.5387 0.0365 0.4249 8 G 0.4050 0.0383 0.5567 9 Q 0.6858 0.0195 0.2947 10 I 0.8642 0.0114 0.1244 11 V 0.8628 0.0248 0.1125 12 C 0.8555 0.0233 0.1211 13 T 0.8061 0.0189 0.1750 14 V 0.6919 0.0237 0.2844 15 R 0.4902 0.0365 0.4733 16 H 0.2843 0.0427 0.6730 17 H 0.0668 0.1548 0.7785 18 G 0.0509 0.1121 0.8370 19 L 0.1071 0.0904 0.8025 20 A 0.1270 0.0900 0.7830 21 H 0.1764 0.0755 0.7481 22 D 0.2683 0.0358 0.6959 23 K 0.5905 0.0151 0.3943 24 L 0.8586 0.0063 0.1351 25 L 0.9041 0.0045 0.0914 26 M 0.9247 0.0034 0.0720 27 V 0.9025 0.0062 0.0913 28 E 0.8460 0.0058 0.1483 29 M 0.7714 0.0064 0.2222 30 I 0.5320 0.0184 0.4495 31 D 0.1854 0.0191 0.7955 32 P 0.0290 0.1346 0.8364 33 Q 0.0469 0.0518 0.9013 34 G 0.0647 0.0550 0.8803 35 N 0.1251 0.0324 0.8425 36 P 0.2788 0.0442 0.6770 37 D 0.1954 0.0503 0.7543 38 G 0.2106 0.0410 0.7484 39 Q 0.3756 0.0269 0.5975 40 C 0.7286 0.0105 0.2609 41 A 0.8843 0.0067 0.1090 42 V 0.9144 0.0047 0.0808 43 A 0.9129 0.0044 0.0827 44 I 0.8911 0.0062 0.1027 45 D 0.7150 0.0097 0.2753 46 N 0.4609 0.0939 0.4452 47 I 0.3449 0.0523 0.6027 48 G 0.3032 0.0668 0.6301 49 A 0.2886 0.0593 0.6521 50 G 0.2250 0.0342 0.7408 51 T 0.0666 0.0618 0.8717 52 G 0.0789 0.0312 0.8899 53 E 0.4675 0.0133 0.5192 54 W 0.8615 0.0034 0.1352 55 V 0.9152 0.0042 0.0806 56 L 0.9286 0.0033 0.0681 57 L 0.9129 0.0043 0.0829 58 V 0.8086 0.0118 0.1796 59 S 0.2823 0.0312 0.6865 60 G 0.0697 0.0866 0.8437 61 S 0.0463 0.5394 0.4143 62 S 0.0235 0.8181 0.1584 63 A 0.0191 0.8385 0.1424 64 R 0.0237 0.8093 0.1669 65 Q 0.0360 0.7330 0.2310 66 A 0.0485 0.5903 0.3612 67 H 0.0749 0.3027 0.6224 68 K 0.0625 0.1342 0.8033 69 S 0.0658 0.1036 0.8306 70 E 0.0506 0.1089 0.8404 71 T 0.0626 0.0670 0.8705 72 S 0.1130 0.0319 0.8551 73 P 0.2153 0.0586 0.7261 74 V 0.3510 0.1221 0.5268 75 D 0.4817 0.1154 0.4030 76 L 0.7083 0.1042 0.1875 77 C 0.8080 0.0703 0.1216 78 V 0.8941 0.0204 0.0855 79 I 0.8592 0.0293 0.1115 80 G 0.8716 0.0158 0.1126 81 I 0.8385 0.0256 0.1359 82 V 0.7992 0.0280 0.1728 83 D 0.7071 0.0509 0.2421 84 E 0.6882 0.0398 0.2720 85 V 0.7464 0.0244 0.2292 86 V 0.6709 0.0230 0.3061 87 S 0.3742 0.0541 0.5717 88 G 0.0640 0.0587 0.8773 89 G 0.0547 0.0655 0.8797 90 Q 0.3619 0.0726 0.5655 91 V 0.7700 0.0283 0.2016 92 I 0.7995 0.0327 0.1677 93 F 0.7208 0.0330 0.2462 94 H 0.4375 0.0381 0.5244 95 K 0.1111 0.0477 0.8412