# This file is the result of combining several RDB files, specifically # T0322.t06.dssp-ebghstl.rdb (weight 1.53986) # T0322.t06.stride-ebghtl.rdb (weight 1.24869) # T0322.t06.str2.rdb (weight 1.54758) # T0322.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 T0322.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0322 # 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 T0322.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 2112 # # ============================================ # Comments from T0322.t06.stride-ebghtl.rdb # ============================================ # TARGET T0322 # 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 T0322.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 2112 # # ============================================ # Comments from T0322.t06.str2.rdb # ============================================ # TARGET T0322 # 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 T0322.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 2112 # # ============================================ # Comments from T0322.t06.alpha.rdb # ============================================ # TARGET T0322 # 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 T0322.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 2112 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0584 0.0263 0.9154 2 S 0.0630 0.0458 0.8912 3 D 0.0331 0.2842 0.6827 4 D 0.0439 0.3238 0.6323 5 L 0.0617 0.3660 0.5724 6 T 0.0700 0.2814 0.6486 7 D 0.0653 0.3173 0.6174 8 A 0.0419 0.4448 0.5133 9 Q 0.0514 0.3952 0.5534 10 T 0.1074 0.3849 0.5077 11 A 0.1476 0.1954 0.6569 12 A 0.1127 0.1496 0.7378 13 I 0.0520 0.4323 0.5158 14 P 0.0196 0.7287 0.2518 15 E 0.0171 0.7702 0.2127 16 G 0.0176 0.7959 0.1866 17 F 0.0175 0.7899 0.1926 18 S 0.0135 0.7280 0.2585 19 Q 0.0150 0.6905 0.2945 20 L 0.0527 0.4691 0.4782 21 N 0.0395 0.4230 0.5375 22 W 0.0406 0.3923 0.5671 23 S 0.0771 0.3160 0.6069 24 R 0.0548 0.3690 0.5762 25 G 0.0620 0.3793 0.5587 26 F 0.0821 0.4459 0.4720 27 G 0.0974 0.4459 0.4568 28 R 0.1034 0.4395 0.4571 29 Q 0.1260 0.3278 0.5462 30 I 0.1372 0.1431 0.7196 31 G 0.0941 0.0515 0.8543 32 P 0.1691 0.0839 0.7470 33 L 0.4048 0.0606 0.5346 34 F 0.6400 0.0327 0.3273 35 E 0.7543 0.0249 0.2208 36 H 0.7112 0.0315 0.2572 37 R 0.7451 0.0187 0.2362 38 E 0.5936 0.0281 0.3783 39 G 0.3232 0.0174 0.6594 40 P 0.0628 0.0573 0.8798 41 G 0.1180 0.0427 0.8392 42 Q 0.8191 0.0125 0.1684 43 A 0.9134 0.0034 0.0831 44 R 0.9263 0.0038 0.0698 45 L 0.9248 0.0034 0.0718 46 A 0.9065 0.0046 0.0889 47 F 0.8670 0.0051 0.1279 48 R 0.7535 0.0059 0.2406 49 V 0.5113 0.0168 0.4719 50 E 0.2787 0.0289 0.6923 51 E 0.0908 0.3851 0.5242 52 H 0.0693 0.3847 0.5460 53 H 0.1183 0.3390 0.5427 54 T 0.1936 0.1525 0.6539 55 N 0.0825 0.0975 0.8200 56 G 0.0613 0.1040 0.8347 57 L 0.0734 0.1206 0.8060 58 G 0.1026 0.1005 0.7970 59 N 0.2014 0.1307 0.6679 60 C 0.2845 0.1782 0.5374 61 H 0.1344 0.3472 0.5184 62 G 0.0276 0.7808 0.1916 63 G 0.0081 0.9332 0.0588 64 M 0.0058 0.9549 0.0393 65 L 0.0053 0.9578 0.0369 66 M 0.0054 0.9559 0.0388 67 S 0.0049 0.9491 0.0460 68 F 0.0048 0.9395 0.0557 69 A 0.0048 0.9499 0.0453 70 D 0.0049 0.9531 0.0420 71 M 0.0048 0.9555 0.0397 72 A 0.0047 0.9530 0.0423 73 W 0.0047 0.9580 0.0373 74 G 0.0047 0.9595 0.0358 75 R 0.0047 0.9571 0.0382 76 I 0.0048 0.9498 0.0454 77 I 0.0063 0.9296 0.0641 78 S 0.0113 0.8725 0.1162 79 L 0.0205 0.7459 0.2336 80 Q 0.0546 0.4419 0.5035 81 K 0.0380 0.2043 0.7578 82 S 0.0445 0.0877 0.8677 83 Y 0.1156 0.0442 0.8402 84 S 0.2934 0.0248 0.6818 85 W 0.7001 0.0121 0.2878 86 V 0.8251 0.0088 0.1661 87 T 0.8847 0.0065 0.1088 88 V 0.8820 0.0103 0.1078 89 R 0.9127 0.0045 0.0828 90 L 0.9023 0.0051 0.0926 91 M 0.8451 0.0065 0.1484 92 C 0.7917 0.0070 0.2013 93 D 0.8060 0.0171 0.1769 94 F 0.7443 0.0212 0.2346 95 L 0.5402 0.0513 0.4085 96 S 0.3461 0.0400 0.6139 97 G 0.2414 0.0312 0.7274 98 A 0.2657 0.0107 0.7237 99 K 0.1372 0.0158 0.8470 100 L 0.0383 0.0754 0.8863 101 G 0.0448 0.0489 0.9063 102 D 0.2752 0.0162 0.7086 103 W 0.7372 0.0034 0.2593 104 V 0.8943 0.0035 0.1022 105 E 0.9230 0.0035 0.0734 106 G 0.9022 0.0052 0.0926 107 E 0.9123 0.0044 0.0834 108 G 0.9077 0.0046 0.0877 109 E 0.8939 0.0059 0.1002 110 L 0.9230 0.0030 0.0740 111 I 0.8374 0.0198 0.1428 112 S 0.8351 0.0050 0.1600 113 E 0.4098 0.0389 0.5513 114 E 0.1265 0.0394 0.8340 115 D 0.1628 0.0284 0.8088 116 M 0.6065 0.0149 0.3786 117 L 0.8945 0.0038 0.1017 118 F 0.9223 0.0036 0.0741 119 T 0.9325 0.0031 0.0645 120 V 0.9277 0.0034 0.0689 121 R 0.9198 0.0034 0.0768 122 G 0.9196 0.0038 0.0766 123 R 0.9276 0.0033 0.0691 124 I 0.9245 0.0036 0.0719 125 W 0.8919 0.0039 0.1042 126 A 0.6979 0.0136 0.2885 127 G 0.0665 0.0224 0.9111 128 E 0.0703 0.0389 0.8909 129 R 0.8087 0.0082 0.1831 130 T 0.9072 0.0036 0.0893 131 L 0.9075 0.0067 0.0858 132 I 0.9212 0.0050 0.0738 133 T 0.9218 0.0048 0.0734 134 G 0.9201 0.0043 0.0756 135 T 0.9135 0.0073 0.0791 136 G 0.9093 0.0050 0.0857 137 V 0.9226 0.0046 0.0728 138 F 0.9236 0.0044 0.0720 139 K 0.9043 0.0065 0.0893 140 A 0.8684 0.0083 0.1233 141 L 0.6180 0.0197 0.3623 142 S 0.3487 0.0312 0.6200 143 A 0.0856 0.1354 0.7789 144 R 0.0596 0.0927 0.8477 145 K 0.0760 0.0227 0.9012 146 P 0.0822 0.0149 0.9029 147 R 0.0841 0.0170 0.8988 148 P 0.0854 0.0525 0.8621 149 G 0.1000 0.0895 0.8105 150 E 0.1918 0.1166 0.6916 151 L 0.1864 0.1011 0.7125 152 A 0.1861 0.1292 0.6847 153 Y 0.1293 0.2354 0.6353 154 K 0.1194 0.2911 0.5895 155 E 0.1201 0.2832 0.5966 156 E 0.0833 0.1700 0.7467 157 A 0.0404 0.0489 0.9107