# This file is the result of combining several RDB files, specifically # T0180.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0180.t2k.stride-ebghtl.rdb (weight 1.24869) # T0180.t2k.str.rdb (weight 1.53983) # T0180.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 T0180.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0180 # 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 T0180.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 1 # # ============================================ # Comments from T0180.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0180 # 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 T0180.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 1 # # ============================================ # Comments from T0180.t2k.str.rdb # ============================================ # TARGET T0180 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0180.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 1 # # ============================================ # Comments from T0180.t2k.alpha.rdb # ============================================ # TARGET T0180 # 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 T0180.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0739 0.0363 0.8898 2 V 0.1934 0.0670 0.7395 3 G 0.1864 0.0634 0.7502 4 R 0.2205 0.0671 0.7124 5 R 0.1704 0.0506 0.7790 6 P 0.1076 0.1007 0.7918 7 G 0.0791 0.0780 0.8428 8 G 0.0860 0.0727 0.8413 9 G 0.1415 0.0956 0.7629 10 L 0.2152 0.1441 0.6407 11 K 0.1925 0.1491 0.6584 12 D 0.1763 0.1201 0.7036 13 T 0.1861 0.0738 0.7401 14 K 0.2395 0.0392 0.7213 15 P 0.3906 0.0347 0.5748 16 V 0.7469 0.0279 0.2251 17 V 0.8510 0.0186 0.1304 18 V 0.8357 0.0279 0.1364 19 R 0.8216 0.0222 0.1563 20 L 0.6451 0.0304 0.3245 21 Y 0.3014 0.0266 0.6720 22 P 0.0598 0.3686 0.5716 23 D 0.0318 0.4910 0.4772 24 E 0.0386 0.6608 0.3006 25 I 0.0489 0.7010 0.2502 26 E 0.0635 0.6942 0.2424 27 A 0.0683 0.6820 0.2497 28 L 0.0725 0.6415 0.2860 29 K 0.0736 0.6051 0.3214 30 S 0.0793 0.4798 0.4409 31 R 0.0987 0.3435 0.5578 32 V 0.1207 0.1577 0.7216 33 P 0.0936 0.1348 0.7716 34 A 0.0632 0.2826 0.6543 35 N 0.0607 0.2884 0.6509 36 T 0.0621 0.3929 0.5450 37 S 0.0780 0.4684 0.4536 38 M 0.0444 0.7184 0.2372 39 S 0.0373 0.8004 0.1623 40 A 0.0398 0.8477 0.1125 41 Y 0.0467 0.8628 0.0905 42 I 0.0575 0.8709 0.0716 43 R 0.0545 0.8792 0.0663 44 R 0.0892 0.8401 0.0707 45 I 0.0954 0.8269 0.0777 46 I 0.1257 0.7742 0.1002 47 L 0.1131 0.7308 0.1561 48 N 0.1193 0.5902 0.2905 49 H 0.1524 0.4402 0.4075 50 L 0.2092 0.3112 0.4796 51 E 0.1677 0.2429 0.5895 52 D 0.1054 0.1687 0.7259 53 D 0.0787 0.1029 0.8184 54 G 0.0762 0.0717 0.8521 55 G 0.0965 0.0664 0.8372 56 G 0.1135 0.0714 0.8151 57 G 0.1170 0.0794 0.8037 58 G 0.1179 0.0889 0.7932 59 G 0.1197 0.1042 0.7761 60 G 0.1195 0.1136 0.7670 61 G 0.1225 0.1087 0.7688 62 G 0.1088 0.1097 0.7815 63 G 0.1161 0.1060 0.7780 64 G 0.1496 0.1097 0.7406 65 G 0.2170 0.1176 0.6654 66 M 0.3465 0.1391 0.5145 67 V 0.3742 0.1193 0.5066 68 G 0.3136 0.0851 0.6014 69 R 0.3256 0.0667 0.6078 70 R 0.2218 0.0486 0.7296 71 P 0.1172 0.1036 0.7792 72 G 0.0806 0.0827 0.8367 73 G 0.0975 0.0809 0.8216 74 G 0.1533 0.0954 0.7513 75 L 0.2352 0.1419 0.6229 76 K 0.2113 0.1421 0.6466 77 D 0.1901 0.1153 0.6946 78 T 0.1976 0.0714 0.7310 79 K 0.2424 0.0386 0.7190 80 P 0.3917 0.0344 0.5739 81 V 0.7469 0.0279 0.2251 82 V 0.8510 0.0186 0.1304 83 V 0.8357 0.0279 0.1364 84 R 0.8216 0.0222 0.1563 85 L 0.6451 0.0304 0.3245 86 Y 0.3014 0.0266 0.6720 87 P 0.0598 0.3686 0.5716 88 D 0.0318 0.4910 0.4772 89 E 0.0386 0.6608 0.3006 90 I 0.0489 0.7010 0.2502 91 E 0.0635 0.6942 0.2424 92 A 0.0683 0.6820 0.2497 93 L 0.0725 0.6415 0.2860 94 K 0.0736 0.6051 0.3214 95 S 0.0793 0.4798 0.4409 96 R 0.0987 0.3435 0.5578 97 V 0.1207 0.1577 0.7216 98 P 0.0936 0.1348 0.7716 99 A 0.0632 0.2826 0.6543 100 N 0.0607 0.2884 0.6509 101 T 0.0621 0.3929 0.5450 102 S 0.0780 0.4684 0.4536 103 M 0.0444 0.7184 0.2372 104 S 0.0368 0.8026 0.1606 105 A 0.0383 0.8509 0.1108 106 Y 0.0428 0.8701 0.0871 107 I 0.0480 0.8840 0.0681 108 R 0.0397 0.8975 0.0628 109 R 0.0503 0.8842 0.0655 110 I 0.0483 0.8803 0.0714 111 I 0.0622 0.8399 0.0980 112 L 0.0481 0.8021 0.1498 113 N 0.0559 0.6703 0.2738 114 H 0.0669 0.5548 0.3783 115 L 0.0907 0.4272 0.4822 116 E 0.0833 0.3215 0.5952 117 D 0.0611 0.1804 0.7585 118 D 0.0410 0.0388 0.9202