# This file is the result of combining several RDB files, specifically # T0353.t04.dssp-ebghstl.rdb (weight 1.53986) # T0353.t04.stride-ebghtl.rdb (weight 1.24869) # T0353.t04.str2.rdb (weight 1.54758) # T0353.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 T0353.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0353 # 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 T0353.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 4.37753 # # ============================================ # Comments from T0353.t04.stride-ebghtl.rdb # ============================================ # TARGET T0353 # 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 T0353.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 4.37753 # # ============================================ # Comments from T0353.t04.str2.rdb # ============================================ # TARGET T0353 # 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 T0353.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 4.37753 # # ============================================ # Comments from T0353.t04.alpha.rdb # ============================================ # TARGET T0353 # 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 T0353.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 4.37753 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3091 0.0083 0.6826 2 Q 0.7829 0.0054 0.2117 3 I 0.8877 0.0038 0.1085 4 H 0.9035 0.0047 0.0918 5 V 0.9116 0.0043 0.0841 6 Y 0.8703 0.0071 0.1226 7 D 0.7866 0.0073 0.2061 8 T 0.6367 0.0322 0.3311 9 Y 0.7789 0.0224 0.1987 10 V 0.8714 0.0113 0.1173 11 K 0.8394 0.0095 0.1511 12 A 0.6170 0.0259 0.3571 13 K 0.1805 0.0668 0.7526 14 D 0.0548 0.0268 0.9184 15 G 0.0903 0.0290 0.8807 16 H 0.4743 0.0109 0.5148 17 V 0.9120 0.0037 0.0843 18 M 0.9053 0.0044 0.0903 19 H 0.9180 0.0036 0.0784 20 F 0.8839 0.0047 0.1114 21 D 0.8395 0.0091 0.1514 22 V 0.8685 0.0098 0.1218 23 F 0.8741 0.0123 0.1135 24 T 0.8026 0.0198 0.1776 25 D 0.5232 0.0185 0.4583 26 V 0.1512 0.1686 0.6802 27 R 0.0732 0.2014 0.7253 28 D 0.0544 0.1836 0.7620 29 D 0.0302 0.5644 0.4054 30 K 0.0098 0.8920 0.0982 31 K 0.0105 0.9280 0.0615 32 A 0.0086 0.9413 0.0500 33 I 0.0052 0.9556 0.0392 34 E 0.0052 0.9563 0.0385 35 F 0.0047 0.9549 0.0404 36 A 0.0047 0.9575 0.0378 37 K 0.0047 0.9599 0.0354 38 Q 0.0048 0.9562 0.0390 39 W 0.0048 0.9489 0.0463 40 L 0.0055 0.9298 0.0647 41 S 0.0064 0.8807 0.1129 42 S 0.0120 0.7788 0.2092 43 I 0.0488 0.4989 0.4523 44 G 0.0554 0.1337 0.8109 45 E 0.0949 0.1779 0.7272 46 E 0.1152 0.1573 0.7274 47 G 0.0833 0.1062 0.8105 48 A 0.1506 0.0566 0.7929 49 T 0.3462 0.0418 0.6121 50 V 0.3365 0.0318 0.6317 51 T 0.2472 0.0426 0.7102 52 S 0.1353 0.2289 0.6358 53 E 0.0856 0.3388 0.5757 54 E 0.1527 0.3480 0.4994 55 C 0.2139 0.2590 0.5271 56 R 0.1590 0.3422 0.4989 57 F 0.2225 0.3371 0.4404 58 C 0.2107 0.3139 0.4754 59 H 0.1320 0.3410 0.5270 60 S 0.0623 0.4950 0.4427 61 Q 0.0378 0.4565 0.5057 62 K 0.0404 0.3208 0.6387 63 A 0.0659 0.0598 0.8743 64 P 0.0481 0.1214 0.8305 65 D 0.0052 0.9257 0.0691 66 E 0.0048 0.9479 0.0472 67 V 0.0049 0.9530 0.0420 68 I 0.0047 0.9597 0.0356 69 E 0.0047 0.9606 0.0347 70 A 0.0047 0.9599 0.0354 71 I 0.0047 0.9545 0.0408 72 K 0.0052 0.9367 0.0581 73 Q 0.0098 0.7902 0.2000 74 N 0.0441 0.1418 0.8141 75 G 0.0532 0.0220 0.9249 76 Y 0.3238 0.0103 0.6660 77 F 0.8774 0.0054 0.1172 78 I 0.9190 0.0055 0.0755 79 Y 0.9039 0.0083 0.0878 80 K 0.8688 0.0087 0.1225 81 M 0.6844 0.0234 0.2922 82 E 0.3722 0.0910 0.5368 83 G 0.1312 0.0765 0.7923 84 C 0.1495 0.0477 0.8028 85 N 0.0834 0.0588 0.8579