# This file is the result of combining several RDB files, specifically # T0288.t06.dssp-ebghstl.rdb (weight 1.53986) # T0288.t06.stride-ebghtl.rdb (weight 1.24869) # T0288.t06.str2.rdb (weight 1.54758) # T0288.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 T0288.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0288 # 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 T0288.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 1801 # # ============================================ # Comments from T0288.t06.stride-ebghtl.rdb # ============================================ # TARGET T0288 # 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 T0288.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 1801 # # ============================================ # Comments from T0288.t06.str2.rdb # ============================================ # TARGET T0288 # 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 T0288.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 1801 # # ============================================ # Comments from T0288.t06.alpha.rdb # ============================================ # TARGET T0288 # 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 T0288.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 1801 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0743 0.0207 0.9051 2 M 0.1417 0.0188 0.8395 3 V 0.2149 0.0121 0.7730 4 P 0.2136 0.0314 0.7550 5 G 0.4441 0.0184 0.5375 6 K 0.8789 0.0050 0.1161 7 V 0.9162 0.0034 0.0804 8 T 0.9178 0.0036 0.0786 9 L 0.9047 0.0036 0.0917 10 Q 0.8400 0.0045 0.1555 11 K 0.6803 0.0171 0.3026 12 D 0.2268 0.0219 0.7513 13 A 0.0449 0.0997 0.8554 14 Q 0.0458 0.0745 0.8797 15 N 0.1123 0.0611 0.8267 16 L 0.3481 0.0381 0.6138 17 I 0.6726 0.0160 0.3114 18 G 0.8231 0.0096 0.1673 19 I 0.9061 0.0042 0.0897 20 S 0.9075 0.0046 0.0878 21 I 0.8759 0.0089 0.1152 22 G 0.6966 0.0198 0.2836 23 G 0.3722 0.0246 0.6032 24 G 0.2017 0.0433 0.7550 25 A 0.1733 0.1334 0.6934 26 Q 0.1452 0.1293 0.7255 27 Y 0.1486 0.0944 0.7570 28 C 0.1389 0.0447 0.8165 29 P 0.1662 0.0482 0.7856 30 C 0.5117 0.0210 0.4673 31 L 0.8442 0.0049 0.1509 32 Y 0.8966 0.0052 0.0982 33 I 0.8978 0.0065 0.0957 34 V 0.8428 0.0281 0.1291 35 Q 0.8610 0.0068 0.1322 36 V 0.7698 0.0127 0.2176 37 F 0.4422 0.0217 0.5361 38 D 0.0857 0.0752 0.8391 39 N 0.0448 0.0497 0.9055 40 T 0.1328 0.0475 0.8196 41 P 0.0746 0.4771 0.4483 42 A 0.0750 0.5700 0.3550 43 A 0.0805 0.5879 0.3315 44 L 0.1124 0.4779 0.4097 45 D 0.0852 0.1611 0.7536 46 G 0.0472 0.0767 0.8761 47 T 0.2192 0.0461 0.7346 48 V 0.4861 0.0193 0.4946 49 A 0.1320 0.0192 0.8488 50 A 0.0360 0.0924 0.8717 51 G 0.0443 0.0368 0.9189 52 D 0.2791 0.0173 0.7036 53 E 0.7975 0.0112 0.1913 54 I 0.8933 0.0114 0.0953 55 T 0.8689 0.0144 0.1168 56 G 0.8905 0.0095 0.1000 57 V 0.8275 0.0215 0.1511 58 N 0.3887 0.0367 0.5746 59 G 0.1396 0.0349 0.8255 60 R 0.6438 0.0147 0.3414 61 S 0.7465 0.0128 0.2407 62 I 0.3952 0.0741 0.5307 63 K 0.1153 0.1040 0.7808 64 G 0.0514 0.0640 0.8846 65 K 0.1926 0.0262 0.7812 66 T 0.1958 0.0369 0.7674 67 K 0.0066 0.9273 0.0660 68 V 0.0047 0.9577 0.0376 69 E 0.0047 0.9597 0.0356 70 V 0.0047 0.9609 0.0344 71 A 0.0047 0.9610 0.0344 72 K 0.0047 0.9605 0.0349 73 M 0.0047 0.9570 0.0383 74 I 0.0051 0.9478 0.0471 75 Q 0.0062 0.9083 0.0855 76 E 0.0107 0.7176 0.2717 77 V 0.0738 0.2674 0.6588 78 K 0.0314 0.1004 0.8682 79 G 0.0775 0.0388 0.8837 80 E 0.5138 0.0180 0.4682 81 V 0.8452 0.0051 0.1497 82 T 0.8869 0.0037 0.1094 83 I 0.8769 0.0040 0.1192 84 H 0.6865 0.0071 0.3064 85 Y 0.3248 0.0192 0.6560 86 N 0.2066 0.0387 0.7547 87 K 0.2051 0.1806 0.6143 88 L 0.3292 0.2218 0.4490 89 Q 0.4198 0.2317 0.3485 90 Y 0.4364 0.2103 0.3534 91 Y 0.4125 0.1640 0.4235 92 K 0.2344 0.1115 0.6541 93 V 0.0569 0.0408 0.9023