# This file is the result of combining several RDB files, specifically # T0306.t04.dssp-ebghstl.rdb (weight 1.53986) # T0306.t04.stride-ebghtl.rdb (weight 1.24869) # T0306.t04.str2.rdb (weight 1.54758) # T0306.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 T0306.t04.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.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 17.5393 # # ============================================ # Comments from T0306.t04.stride-ebghtl.rdb # ============================================ # TARGET T0306 # 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 T0306.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 17.5393 # # ============================================ # Comments from T0306.t04.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.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 17.5393 # # ============================================ # Comments from T0306.t04.alpha.rdb # ============================================ # TARGET T0306 # 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 T0306.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 17.5393 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1640 0.0141 0.8219 2 K 0.5245 0.0180 0.4575 3 L 0.7686 0.0271 0.2043 4 A 0.8267 0.0236 0.1497 5 V 0.8706 0.0224 0.1070 6 V 0.8584 0.0102 0.1313 7 T 0.6228 0.0267 0.3505 8 G 0.3805 0.0420 0.5776 9 Q 0.6703 0.0225 0.3071 10 I 0.8969 0.0047 0.0984 11 V 0.8941 0.0077 0.0982 12 C 0.8559 0.0129 0.1311 13 T 0.7242 0.0355 0.2403 14 V 0.6380 0.0387 0.3232 15 R 0.5307 0.0493 0.4200 16 H 0.2486 0.0818 0.6696 17 H 0.0670 0.1882 0.7448 18 G 0.0634 0.1720 0.7646 19 L 0.1311 0.1441 0.7248 20 A 0.1122 0.1282 0.7596 21 H 0.1060 0.1372 0.7568 22 D 0.1815 0.0988 0.7197 23 K 0.4517 0.0639 0.4844 24 L 0.7838 0.0128 0.2034 25 L 0.8919 0.0058 0.1022 26 M 0.9195 0.0042 0.0763 27 V 0.8943 0.0054 0.1003 28 E 0.8737 0.0060 0.1203 29 M 0.8423 0.0068 0.1510 30 I 0.6844 0.0170 0.2985 31 D 0.1531 0.0157 0.8312 32 P 0.0148 0.1385 0.8468 33 Q 0.0491 0.0525 0.8984 34 G 0.0634 0.0540 0.8826 35 N 0.1044 0.0224 0.8731 36 P 0.1618 0.0881 0.7500 37 D 0.0922 0.0821 0.8257 38 G 0.1402 0.0548 0.8049 39 Q 0.3217 0.0180 0.6603 40 C 0.7214 0.0049 0.2738 41 A 0.8849 0.0042 0.1109 42 V 0.9252 0.0036 0.0712 43 A 0.9229 0.0040 0.0731 44 I 0.8912 0.0074 0.1013 45 D 0.6837 0.0168 0.2996 46 N 0.3752 0.0442 0.5806 47 I 0.2124 0.0556 0.7321 48 G 0.1860 0.0395 0.7744 49 A 0.1570 0.0311 0.8119 50 G 0.1138 0.0330 0.8533 51 T 0.0463 0.0489 0.9048 52 G 0.0490 0.0353 0.9157 53 E 0.3049 0.0192 0.6758 54 W 0.8453 0.0035 0.1512 55 V 0.9250 0.0034 0.0716 56 L 0.9289 0.0034 0.0677 57 L 0.9119 0.0047 0.0833 58 V 0.7400 0.0142 0.2458 59 S 0.2707 0.0405 0.6888 60 G 0.0771 0.0796 0.8433 61 S 0.0476 0.4622 0.4902 62 S 0.0375 0.7071 0.2555 63 A 0.0264 0.7924 0.1813 64 R 0.0341 0.7900 0.1759 65 Q 0.0419 0.7311 0.2270 66 A 0.0445 0.6310 0.3245 67 H 0.0668 0.4209 0.5123 68 K 0.0510 0.2125 0.7365 69 S 0.0558 0.1042 0.8400 70 E 0.0370 0.1106 0.8524 71 T 0.0636 0.0693 0.8671 72 S 0.0922 0.0363 0.8715 73 P 0.1646 0.0888 0.7466 74 V 0.3859 0.0901 0.5240 75 D 0.4521 0.0758 0.4720 76 L 0.7949 0.0391 0.1660 77 C 0.8764 0.0198 0.1037 78 V 0.9064 0.0182 0.0754 79 I 0.8973 0.0200 0.0827 80 G 0.8989 0.0121 0.0890 81 I 0.9004 0.0121 0.0875 82 V 0.8341 0.0213 0.1447 83 D 0.7295 0.0346 0.2358 84 E 0.6013 0.0498 0.3489 85 V 0.6393 0.0617 0.2991 86 V 0.5261 0.0588 0.4151 87 S 0.2591 0.0890 0.6519 88 G 0.0696 0.0414 0.8890 89 G 0.0938 0.0387 0.8675 90 Q 0.4552 0.0368 0.5080 91 V 0.7569 0.0251 0.2180 92 I 0.7567 0.0305 0.2128 93 F 0.6812 0.0351 0.2837 94 H 0.3784 0.0284 0.5932 95 K 0.1132 0.0335 0.8533