# This file is the result of combining several RDB files, specifically # T0205.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0205.t2k.stride-ebghtl.rdb (weight 1.24869) # T0205.t2k.str2.rdb (weight 1.54758) # T0205.t2k.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 T0205.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0205 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0205.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 22 # # ============================================ # Comments from T0205.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0205 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0205.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 22 # # ============================================ # Comments from T0205.t2k.str2.rdb # ============================================ # TARGET T0205 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0205.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 22 # # ============================================ # Comments from T0205.t2k.alpha.rdb # ============================================ # TARGET T0205 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0205.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 22 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1436 0.2225 0.6339 2 E 0.1948 0.3466 0.4585 3 E 0.2694 0.3319 0.3987 4 I 0.2445 0.3715 0.3840 5 T 0.1908 0.2967 0.5125 6 D 0.1068 0.3054 0.5877 7 G 0.1045 0.2496 0.6459 8 V 0.2056 0.1700 0.6244 9 N 0.2715 0.1365 0.5920 10 N 0.3844 0.1126 0.5030 11 M 0.5747 0.0849 0.3404 12 N 0.7388 0.0533 0.2079 13 L 0.7772 0.0419 0.1809 14 A 0.7570 0.0338 0.2092 15 T 0.6391 0.0320 0.3289 16 D 0.4917 0.0285 0.4798 17 S 0.3379 0.0618 0.6003 18 Q 0.1930 0.0761 0.7308 19 K 0.1534 0.0778 0.7687 20 K 0.1407 0.0844 0.7749 21 N 0.2349 0.0488 0.7163 22 R 0.7340 0.0139 0.2522 23 I 0.8662 0.0080 0.1258 24 Q 0.8858 0.0054 0.1088 25 V 0.8082 0.0118 0.1800 26 S 0.3845 0.0240 0.5915 27 N 0.1020 0.0646 0.8334 28 T 0.0917 0.0390 0.8693 29 K 0.0703 0.0480 0.8817 30 K 0.0745 0.0620 0.8634 31 P 0.1541 0.2700 0.5759 32 L 0.1170 0.6113 0.2717 33 F 0.0860 0.7536 0.1604 34 F 0.0682 0.7949 0.1368 35 Y 0.0241 0.9084 0.0675 36 V 0.0181 0.9328 0.0491 37 N 0.0133 0.9374 0.0493 38 L 0.0143 0.9358 0.0499 39 A 0.0189 0.9264 0.0547 40 K 0.0206 0.9171 0.0623 41 R 0.0165 0.8775 0.1061 42 Y 0.0196 0.8275 0.1529 43 M 0.0416 0.6609 0.2975 44 Q 0.0364 0.4461 0.5175 45 Q 0.0485 0.1666 0.7849 46 Y 0.0961 0.0449 0.8590 47 N 0.0770 0.0815 0.8415 48 D 0.6638 0.0379 0.2983 49 V 0.8723 0.0199 0.1079 50 E 0.8840 0.0222 0.0938 51 L 0.8299 0.0413 0.1287 52 S 0.6469 0.0924 0.2607 53 A 0.4478 0.1814 0.3708 54 L 0.2608 0.3124 0.4268 55 G 0.1925 0.3757 0.4317 56 M 0.2064 0.5139 0.2797 57 A 0.1394 0.6556 0.2050 58 I 0.0713 0.7949 0.1339 59 A 0.0305 0.8261 0.1433 60 T 0.0188 0.8355 0.1457 61 V 0.0262 0.8627 0.1111 62 V 0.0252 0.8719 0.1030 63 T 0.0258 0.8760 0.0982 64 V 0.0054 0.9520 0.0426 65 T 0.0047 0.9572 0.0381 66 E 0.0048 0.9547 0.0405 67 I 0.0055 0.9451 0.0494 68 L 0.0068 0.9303 0.0629 69 K 0.0102 0.8888 0.1010 70 N 0.0234 0.6943 0.2823 71 N 0.0481 0.3399 0.6120 72 G 0.0957 0.1652 0.7391 73 F 0.2358 0.1332 0.6310 74 A 0.4343 0.1145 0.4513 75 V 0.5939 0.0775 0.3285 76 E 0.7302 0.0372 0.2326 77 K 0.7240 0.0376 0.2384 78 K 0.7567 0.0221 0.2213 79 I 0.7366 0.0216 0.2418 80 M 0.7117 0.0213 0.2670 81 T 0.6118 0.0385 0.3497 82 S 0.6290 0.0563 0.3148 83 I 0.7311 0.0338 0.2351 84 V 0.6992 0.0263 0.2744 85 D 0.5780 0.0279 0.3941 86 I 0.3722 0.0676 0.5602 87 K 0.1915 0.0903 0.7182 88 D 0.1438 0.1138 0.7424 89 D 0.1180 0.1875 0.6945 90 A 0.1368 0.1707 0.6925 91 R 0.1488 0.1066 0.7446 92 G 0.1523 0.0585 0.7892 93 R 0.2702 0.0337 0.6961 94 P 0.4441 0.0360 0.5199 95 V 0.5552 0.0401 0.4047 96 Q 0.6403 0.0228 0.3369 97 K 0.6980 0.0249 0.2771 98 A 0.7273 0.0212 0.2515 99 K 0.8650 0.0088 0.1262 100 I 0.9139 0.0046 0.0815 101 E 0.9191 0.0045 0.0764 102 I 0.9201 0.0032 0.0766 103 T 0.9001 0.0055 0.0944 104 L 0.8424 0.0129 0.1447 105 V 0.6577 0.0256 0.3168 106 K 0.3700 0.0360 0.5939 107 S 0.1118 0.0442 0.8440 108 E 0.0138 0.6249 0.3613 109 K 0.0091 0.7833 0.2076 110 F 0.0081 0.8738 0.1181 111 D 0.0069 0.8922 0.1009 112 E 0.0069 0.8908 0.1023 113 L 0.0084 0.8763 0.1154 114 M 0.0094 0.8608 0.1298 115 A 0.0080 0.8608 0.1312 116 A 0.0065 0.8494 0.1441 117 A 0.0093 0.8363 0.1544 118 N 0.0161 0.7513 0.2326 119 E 0.0247 0.6727 0.3026 120 E 0.0342 0.6220 0.3438 121 K 0.0265 0.6945 0.2790 122 E 0.0184 0.7816 0.2000 123 D 0.0103 0.8882 0.1016 124 A 0.0100 0.8909 0.0991 125 E 0.0107 0.8925 0.0968 126 T 0.0124 0.8742 0.1134 127 Q 0.0144 0.8272 0.1584 128 V 0.0227 0.6646 0.3127 129 Q 0.0350 0.4182 0.5467 130 N 0.0417 0.0474 0.9109