# This file is the result of combining several RDB files, specifically # T0321.t04.dssp-ebghstl.rdb (weight 1.53986) # T0321.t04.stride-ebghtl.rdb (weight 1.24869) # T0321.t04.str2.rdb (weight 1.54758) # T0321.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 T0321.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-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 T0321.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 49.5759 # # ============================================ # Comments from T0321.t04.stride-ebghtl.rdb # ============================================ # TARGET T0321 # 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 T0321.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 49.5759 # # ============================================ # Comments from T0321.t04.str2.rdb # ============================================ # TARGET T0321 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0321.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 49.5759 # # ============================================ # Comments from T0321.t04.alpha.rdb # ============================================ # TARGET T0321 # 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 T0321.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 49.5759 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 V 0.1019 0.0356 0.8625 2 E 0.1031 0.0712 0.8257 3 D 0.0843 0.1724 0.7433 4 R 0.0734 0.1719 0.7547 5 M 0.0852 0.1616 0.7531 6 N 0.0618 0.0864 0.8518 7 D 0.0761 0.0887 0.8352 8 P 0.0442 0.3933 0.5626 9 F 0.0616 0.4625 0.4759 10 I 0.1056 0.4463 0.4481 11 M 0.1603 0.3984 0.4414 12 S 0.1444 0.4544 0.4012 13 Q 0.1113 0.5270 0.3617 14 N 0.1327 0.5341 0.3332 15 E 0.1198 0.5465 0.3337 16 V 0.1534 0.2931 0.5536 17 K 0.0501 0.0902 0.8597 18 G 0.0313 0.0383 0.9304 19 K 0.1842 0.0151 0.8007 20 K 0.7476 0.0040 0.2485 21 V 0.9201 0.0040 0.0760 22 G 0.9308 0.0034 0.0658 23 V 0.9291 0.0033 0.0676 24 V 0.8688 0.0222 0.1090 25 G 0.5896 0.0170 0.3934 26 H 0.2468 0.0349 0.7182 27 F 0.1200 0.0857 0.7942 28 P 0.0608 0.2847 0.6545 29 H 0.0644 0.4098 0.5258 30 L 0.0187 0.7790 0.2023 31 E 0.0150 0.8132 0.1719 32 S 0.0139 0.7822 0.2038 33 L 0.0731 0.5900 0.3369 34 L 0.1166 0.3701 0.5133 35 E 0.1077 0.2314 0.6609 36 P 0.1033 0.2463 0.6503 37 I 0.1822 0.1986 0.6192 38 C 0.2367 0.0744 0.6889 39 D 0.4836 0.0294 0.4871 40 L 0.7626 0.0074 0.2300 41 S 0.8584 0.0088 0.1328 42 I 0.8964 0.0115 0.0921 43 L 0.8651 0.0143 0.1205 44 E 0.7977 0.0113 0.1910 45 W 0.5189 0.0175 0.4636 46 S 0.1990 0.0152 0.7858 47 P 0.0496 0.1088 0.8417 48 E 0.0468 0.0843 0.8689 49 E 0.0454 0.1057 0.8489 50 G 0.0418 0.0594 0.8988 51 D 0.1540 0.0463 0.7998 52 Y 0.1731 0.0191 0.8078 53 P 0.1164 0.0334 0.8503 54 L 0.0499 0.3944 0.5557 55 P 0.0233 0.5907 0.3859 56 A 0.0157 0.7666 0.2176 57 S 0.0304 0.7446 0.2250 58 E 0.0175 0.6358 0.3468 59 F 0.0300 0.4611 0.5090 60 I 0.0677 0.4473 0.4850 61 L 0.0684 0.1575 0.7742 62 P 0.0159 0.3293 0.6548 63 E 0.0325 0.2294 0.7381 64 C 0.1742 0.0843 0.7415 65 D 0.1622 0.0673 0.7706 66 Y 0.8324 0.0325 0.1351 67 V 0.9120 0.0143 0.0737 68 Y 0.9072 0.0255 0.0673 69 I 0.8068 0.0688 0.1244 70 T 0.4956 0.1190 0.3853 71 C 0.2050 0.4557 0.3393 72 A 0.0867 0.6155 0.2978 73 S 0.0756 0.7644 0.1600 74 V 0.0819 0.7998 0.1183 75 V 0.0746 0.7333 0.1921 76 D 0.0619 0.5680 0.3701 77 K 0.0173 0.5470 0.4357 78 T 0.0255 0.6415 0.3330 79 L 0.0049 0.9434 0.0517 80 P 0.0048 0.9527 0.0425 81 R 0.0047 0.9537 0.0416 82 L 0.0048 0.9536 0.0417 83 L 0.0048 0.9368 0.0584 84 E 0.0053 0.8718 0.1230 85 L 0.0084 0.7833 0.2083 86 S 0.0260 0.5581 0.4159 87 R 0.0172 0.4669 0.5158 88 N 0.0306 0.2739 0.6955 89 A 0.1047 0.1266 0.7687 90 R 0.3511 0.0386 0.6102 91 R 0.8252 0.0087 0.1661 92 I 0.9219 0.0035 0.0746 93 T 0.9297 0.0034 0.0669 94 L 0.9229 0.0037 0.0734 95 V 0.8110 0.0140 0.1750 96 G 0.2967 0.0166 0.6867 97 P 0.1177 0.0581 0.8242 98 G 0.0956 0.1002 0.8041 99 T 0.0726 0.1876 0.7399 100 P 0.0473 0.3967 0.5560 101 L 0.0643 0.4588 0.4769 102 A 0.0491 0.4287 0.5222 103 P 0.0150 0.8355 0.1495 104 V 0.0132 0.8569 0.1299 105 L 0.0107 0.8838 0.1055 106 F 0.0129 0.8349 0.1522 107 E 0.0125 0.7147 0.2728 108 H 0.0412 0.4681 0.4907 109 G 0.0620 0.0892 0.8488 110 L 0.1992 0.1136 0.6872 111 Q 0.3435 0.1333 0.5232 112 E 0.6969 0.1198 0.1833 113 L 0.8038 0.0618 0.1344 114 S 0.7364 0.0640 0.1996 115 G 0.6211 0.0443 0.3347 116 F 0.6360 0.0217 0.3422 117 M 0.7125 0.0187 0.2688 118 V 0.6271 0.0177 0.3553 119 K 0.3116 0.0410 0.6475 120 D 0.1183 0.0431 0.8385 121 N 0.0061 0.8932 0.1007 122 A 0.0074 0.9363 0.0563 123 R 0.0070 0.9399 0.0530 124 A 0.0062 0.9538 0.0400 125 F 0.0080 0.9528 0.0392 126 R 0.0100 0.9511 0.0389 127 I 0.0120 0.9455 0.0426 128 V 0.0135 0.9236 0.0629 129 A 0.0264 0.8019 0.1716 130 G 0.0372 0.4628 0.5000 131 A 0.0630 0.2597 0.6773 132 E 0.0742 0.1982 0.7277 133 K 0.1747 0.1825 0.6427 134 V 0.3320 0.1296 0.5384 135 K 0.5224 0.0915 0.3861 136 I 0.5680 0.1003 0.3318 137 Y 0.4549 0.0904 0.4547 138 S 0.3221 0.0892 0.5887 139 A 0.1732 0.0996 0.7273 140 G 0.3459 0.0457 0.6085 141 Q 0.6730 0.0156 0.3114 142 K 0.8811 0.0058 0.1131 143 V 0.8937 0.0053 0.1010 144 T 0.9148 0.0051 0.0801 145 I 0.8781 0.0072 0.1146 146 K 0.6801 0.0196 0.3002 147 K 0.2613 0.0248 0.7139