# This file is the result of combining several RDB files, specifically # T0350.t06.dssp-ebghstl.rdb (weight 1.53986) # T0350.t06.stride-ebghtl.rdb (weight 1.24869) # T0350.t06.str2.rdb (weight 1.54758) # T0350.t06.alpha.rdb (weight 0.659012) # T0350.t04.dssp-ebghstl.rdb (weight 1.53986) # T0350.t04.stride-ebghtl.rdb (weight 1.24869) # T0350.t04.str2.rdb (weight 1.54758) # T0350.t04.alpha.rdb (weight 0.659012) # T0350.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0350.t2k.stride-ebghtl.rdb (weight 1.24869) # T0350.t2k.str2.rdb (weight 1.54758) # T0350.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 T0350.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0350 # 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 T0350.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 127 # # ============================================ # Comments from T0350.t06.stride-ebghtl.rdb # ============================================ # TARGET T0350 # 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 T0350.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 127 # # ============================================ # Comments from T0350.t06.str2.rdb # ============================================ # TARGET T0350 # 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 T0350.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 127 # # ============================================ # Comments from T0350.t06.alpha.rdb # ============================================ # TARGET T0350 # 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 T0350.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 127 # # ============================================ # Comments from T0350.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0350 # 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 T0350.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 127 # # ============================================ # Comments from T0350.t04.stride-ebghtl.rdb # ============================================ # TARGET T0350 # 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 T0350.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 127 # # ============================================ # Comments from T0350.t04.str2.rdb # ============================================ # TARGET T0350 # Using neural net t04-2621-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 T0350.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 127 # # ============================================ # Comments from T0350.t04.alpha.rdb # ============================================ # TARGET T0350 # 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 T0350.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 127 # # ============================================ # Comments from T0350.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0350 # 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 T0350.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 114 # # ============================================ # Comments from T0350.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0350 # 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 T0350.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 114 # # ============================================ # Comments from T0350.t2k.str2.rdb # ============================================ # TARGET T0350 # 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 T0350.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 114 # # ============================================ # Comments from T0350.t2k.alpha.rdb # ============================================ # TARGET T0350 # 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 T0350.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 114 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1317 0.0302 0.8381 2 N 0.1866 0.0396 0.7738 3 I 0.3127 0.1106 0.5767 4 E 0.3149 0.1395 0.5456 5 R 0.3080 0.1350 0.5570 6 L 0.2712 0.1281 0.6007 7 T 0.2513 0.1298 0.6189 8 T 0.2340 0.0712 0.6948 9 L 0.1496 0.0814 0.7690 10 Q 0.1412 0.0809 0.7779 11 P 0.1370 0.1591 0.7038 12 V 0.1298 0.1993 0.6710 13 W 0.1235 0.1662 0.7103 14 D 0.1023 0.1738 0.7239 15 R 0.0615 0.3782 0.5603 16 Y 0.0644 0.4210 0.5146 17 D 0.0796 0.4413 0.4790 18 T 0.0732 0.4434 0.4834 19 Q 0.0814 0.4168 0.5018 20 I 0.0837 0.4725 0.4439 21 H 0.0688 0.5327 0.3984 22 N 0.0517 0.5933 0.3550 23 Q 0.0431 0.6359 0.3210 24 K 0.0412 0.6711 0.2877 25 D 0.0401 0.6696 0.2903 26 N 0.0343 0.6800 0.2857 27 D 0.0349 0.6352 0.3299 28 N 0.0465 0.5446 0.4090 29 E 0.0456 0.4946 0.4598 30 V 0.0583 0.4492 0.4925 31 P 0.0509 0.4242 0.5249 32 V 0.0537 0.4266 0.5196 33 H 0.0731 0.3813 0.5456 34 Q 0.1094 0.2841 0.6065 35 V 0.1158 0.1703 0.7140 36 S 0.0884 0.1172 0.7944 37 Y 0.0059 0.8982 0.0958 38 T 0.0053 0.9209 0.0738 39 N 0.0054 0.9287 0.0659 40 L 0.0048 0.9479 0.0473 41 A 0.0047 0.9553 0.0400 42 E 0.0047 0.9553 0.0400 43 M 0.0047 0.9557 0.0396 44 V 0.0047 0.9562 0.0390 45 G 0.0048 0.9537 0.0414 46 E 0.0049 0.9507 0.0444 47 M 0.0050 0.9500 0.0450 48 N 0.0050 0.9464 0.0486 49 K 0.0055 0.9326 0.0619 50 L 0.0065 0.9001 0.0934 51 L 0.0158 0.8296 0.1545 52 E 0.0229 0.7187 0.2584 53 P 0.0343 0.5893 0.3764 54 S 0.0799 0.3335 0.5866 55 Q 0.1058 0.1236 0.7706 56 V 0.2535 0.0726 0.6739 57 H 0.5409 0.0228 0.4363 58 L 0.7409 0.0093 0.2497 59 K 0.8591 0.0056 0.1353 60 F 0.8880 0.0043 0.1077 61 E 0.8908 0.0041 0.1051 62 L 0.8482 0.0060 0.1458 63 H 0.5718 0.0146 0.4136 64 D 0.0389 0.1832 0.7780 65 K 0.0210 0.1812 0.7978 66 L 0.0685 0.0973 0.8342 67 N 0.0801 0.0347 0.8852 68 E 0.5994 0.0079 0.3926 69 Y 0.8608 0.0034 0.1358 70 Y 0.9138 0.0060 0.0802 71 V 0.9217 0.0038 0.0745 72 K 0.9188 0.0041 0.0771 73 V 0.9257 0.0030 0.0713 74 I 0.8827 0.0061 0.1112 75 E 0.7533 0.0044 0.2423 76 D 0.0367 0.1290 0.8343 77 S 0.0251 0.1004 0.8745 78 T 0.0764 0.0504 0.8732 79 N 0.0977 0.1097 0.7925 80 E 0.5288 0.0990 0.3722 81 V 0.7477 0.0828 0.1695 82 I 0.6851 0.1060 0.2089 83 R 0.6862 0.1147 0.1992 84 E 0.5598 0.1185 0.3217 85 I 0.3289 0.0527 0.6185 86 P 0.0905 0.0244 0.8850 87 P 0.0318 0.5821 0.3861 88 K 0.0057 0.8955 0.0988 89 R 0.0056 0.9228 0.0716 90 W 0.0050 0.9412 0.0538 91 L 0.0047 0.9542 0.0410 92 D 0.0048 0.9549 0.0404 93 F 0.0047 0.9560 0.0393 94 Y 0.0047 0.9566 0.0387 95 A 0.0048 0.9500 0.0452 96 A 0.0053 0.9381 0.0566 97 M 0.0059 0.9328 0.0614 98 T 0.0056 0.9127 0.0818 99 E 0.0067 0.8502 0.1431 100 F 0.0195 0.7764 0.2041 101 L 0.0304 0.7105 0.2591 102 G 0.0553 0.5361 0.4086 103 L 0.1521 0.5575 0.2904 104 F 0.2543 0.5163 0.2294 105 V 0.2455 0.4715 0.2830 106 D 0.1800 0.3651 0.4550 107 E 0.0398 0.7300 0.2302 108 K 0.0368 0.7554 0.2078 109 K 0.0496 0.7511 0.1993 110 L 0.0629 0.7050 0.2321 111 E 0.0862 0.5852 0.3286 112 H 0.0570 0.5300 0.4130 113 H 0.0611 0.3578 0.5810 114 H 0.0772 0.2603 0.6625 115 H 0.0731 0.1631 0.7638 116 H 0.0781 0.0964 0.8255 117 H 0.0480 0.0410 0.9110