# This file is the result of combining several RDB files, specifically # T0306.t06.dssp-ebghstl.rdb (weight 1.53986) # T0306.t06.stride-ebghtl.rdb (weight 1.24869) # T0306.t06.str2.rdb (weight 1.54758) # T0306.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 T0306.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0306 # 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 T0306.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 17.5341 # # ============================================ # Comments from T0306.t06.stride-ebghtl.rdb # ============================================ # TARGET T0306 # 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 T0306.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 17.5341 # # ============================================ # Comments from T0306.t06.str2.rdb # ============================================ # TARGET T0306 # 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 T0306.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 17.5341 # # ============================================ # Comments from T0306.t06.alpha.rdb # ============================================ # TARGET T0306 # 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 T0306.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 17.5341 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1570 0.0151 0.8279 2 K 0.5344 0.0191 0.4465 3 L 0.7847 0.0276 0.1877 4 A 0.8407 0.0206 0.1387 5 V 0.8734 0.0233 0.1033 6 V 0.8745 0.0111 0.1143 7 T 0.6582 0.0255 0.3162 8 G 0.3869 0.0383 0.5748 9 Q 0.6814 0.0189 0.2997 10 I 0.8913 0.0052 0.1035 11 V 0.8903 0.0083 0.1014 12 C 0.8590 0.0116 0.1294 13 T 0.7471 0.0257 0.2272 14 V 0.6661 0.0343 0.2996 15 R 0.5426 0.0492 0.4083 16 H 0.2507 0.0726 0.6766 17 H 0.0634 0.1943 0.7423 18 G 0.0533 0.1673 0.7793 19 L 0.1297 0.1494 0.7208 20 A 0.1140 0.1316 0.7544 21 H 0.1004 0.1379 0.7618 22 D 0.1754 0.1064 0.7182 23 K 0.4012 0.0767 0.5221 24 L 0.7636 0.0171 0.2194 25 L 0.8808 0.0078 0.1115 26 M 0.9162 0.0053 0.0785 27 V 0.8939 0.0054 0.1007 28 E 0.8716 0.0064 0.1220 29 M 0.8496 0.0058 0.1446 30 I 0.6793 0.0149 0.3058 31 D 0.1592 0.0134 0.8274 32 P 0.0148 0.1534 0.8318 33 Q 0.0468 0.0717 0.8815 34 G 0.0618 0.0651 0.8731 35 N 0.1044 0.0228 0.8729 36 P 0.1548 0.0927 0.7525 37 D 0.0839 0.0881 0.8280 38 G 0.1218 0.0607 0.8175 39 Q 0.2895 0.0199 0.6906 40 C 0.6955 0.0057 0.2989 41 A 0.8824 0.0042 0.1134 42 V 0.9249 0.0034 0.0717 43 A 0.9220 0.0041 0.0739 44 I 0.8896 0.0070 0.1033 45 D 0.6597 0.0205 0.3198 46 N 0.3599 0.0402 0.5999 47 I 0.2051 0.0657 0.7292 48 G 0.1792 0.0352 0.7856 49 A 0.1633 0.0305 0.8062 50 G 0.1241 0.0275 0.8484 51 T 0.0459 0.0555 0.8986 52 G 0.0527 0.0367 0.9106 53 E 0.3689 0.0140 0.6171 54 W 0.8529 0.0034 0.1438 55 V 0.9268 0.0033 0.0700 56 L 0.9298 0.0033 0.0669 57 L 0.9116 0.0050 0.0834 58 V 0.7432 0.0139 0.2429 59 S 0.3002 0.0368 0.6630 60 G 0.0894 0.0693 0.8413 61 S 0.0548 0.4341 0.5112 62 S 0.0385 0.6919 0.2697 63 A 0.0279 0.7841 0.1880 64 R 0.0354 0.7853 0.1793 65 Q 0.0443 0.7253 0.2304 66 A 0.0475 0.6350 0.3175 67 H 0.0666 0.4361 0.4972 68 K 0.0542 0.2216 0.7242 69 S 0.0580 0.1211 0.8209 70 E 0.0425 0.1080 0.8495 71 T 0.0645 0.0680 0.8676 72 S 0.0895 0.0327 0.8778 73 P 0.1718 0.0920 0.7362 74 V 0.4141 0.0772 0.5086 75 D 0.4678 0.0660 0.4662 76 L 0.8020 0.0255 0.1725 77 C 0.8842 0.0106 0.1052 78 V 0.9181 0.0072 0.0747 79 I 0.9038 0.0149 0.0814 80 G 0.9009 0.0109 0.0883 81 I 0.9002 0.0119 0.0879 82 V 0.8266 0.0213 0.1521 83 D 0.7112 0.0316 0.2572 84 E 0.6067 0.0495 0.3439 85 V 0.6432 0.0626 0.2943 86 V 0.5172 0.0577 0.4251 87 S 0.2592 0.0932 0.6475 88 G 0.0702 0.0437 0.8861 89 G 0.0865 0.0422 0.8713 90 Q 0.4410 0.0408 0.5182 91 V 0.7494 0.0265 0.2241 92 I 0.7563 0.0339 0.2098 93 F 0.6684 0.0398 0.2919 94 H 0.3421 0.0331 0.6248 95 K 0.0717 0.0357 0.8926