# This file is the result of combining several RDB files, specifically # T0242.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0242.t2k.stride-ebghtl.rdb (weight 1.24869) # T0242.t2k.str2.rdb (weight 1.54758) # T0242.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 T0242.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0242 # 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 T0242.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 5 # # ============================================ # Comments from T0242.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0242 # 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 T0242.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 5 # # ============================================ # Comments from T0242.t2k.str2.rdb # ============================================ # TARGET T0242 # 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 T0242.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 5 # # ============================================ # Comments from T0242.t2k.alpha.rdb # ============================================ # TARGET T0242 # 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 T0242.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 5 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1308 0.0613 0.8079 2 G 0.1985 0.0336 0.7679 3 K 0.5720 0.0318 0.3961 4 V 0.8605 0.0135 0.1260 5 F 0.8887 0.0127 0.0987 6 L 0.8900 0.0129 0.0971 7 T 0.7616 0.0464 0.1921 8 N 0.5163 0.0675 0.4162 9 A 0.3519 0.1552 0.4929 10 F 0.3512 0.1324 0.5165 11 S 0.2260 0.1457 0.6283 12 I 0.0779 0.5423 0.3798 13 N 0.0630 0.5589 0.3780 14 M 0.0620 0.5487 0.3893 15 L 0.0828 0.3921 0.5251 16 K 0.0425 0.2420 0.7155 17 E 0.0370 0.1051 0.8578 18 F 0.0869 0.0301 0.8829 19 P 0.1517 0.0362 0.8121 20 T 0.6506 0.0167 0.3327 21 T 0.8784 0.0072 0.1144 22 I 0.8979 0.0065 0.0957 23 T 0.8628 0.0078 0.1294 24 I 0.5832 0.0944 0.3224 25 D 0.2678 0.1750 0.5573 26 K 0.2123 0.1895 0.5982 27 L 0.2394 0.0845 0.6761 28 D 0.1629 0.0944 0.7427 29 E 0.0286 0.7552 0.2162 30 E 0.0224 0.8090 0.1686 31 D 0.0173 0.8443 0.1384 32 F 0.0279 0.7705 0.2015 33 C 0.0337 0.7256 0.2407 34 L 0.0317 0.6346 0.3337 35 K 0.0474 0.4933 0.4593 36 L 0.0894 0.4331 0.4775 37 E 0.1214 0.3722 0.5064 38 L 0.1435 0.3303 0.5262 39 R 0.1554 0.2511 0.5934 40 L 0.1103 0.1376 0.7521 41 E 0.0982 0.1694 0.7324 42 D 0.0865 0.1794 0.7341 43 G 0.0258 0.6170 0.3572 44 T 0.0590 0.6795 0.2615 45 L 0.1192 0.7097 0.1711 46 I 0.1504 0.6480 0.2016 47 N 0.1669 0.5973 0.2358 48 A 0.1757 0.5976 0.2267 49 I 0.1319 0.4885 0.3797 50 G 0.0884 0.3360 0.5756 51 H 0.0497 0.4894 0.4610 52 D 0.0089 0.8928 0.0984 53 S 0.0070 0.9299 0.0631 54 T 0.0048 0.9518 0.0433 55 I 0.0047 0.9592 0.0361 56 N 0.0047 0.9591 0.0361 57 L 0.0048 0.9568 0.0385 58 V 0.0048 0.9548 0.0404 59 N 0.0051 0.9444 0.0505 60 T 0.0061 0.9181 0.0758 61 L 0.0094 0.8658 0.1248 62 C 0.0319 0.6396 0.3286 63 G 0.0269 0.3279 0.6452 64 T 0.0855 0.2091 0.7054 65 Q 0.2295 0.1553 0.6152 66 L 0.2025 0.2040 0.5935 67 Q 0.2265 0.2043 0.5692 68 K 0.2351 0.1901 0.5748 69 N 0.3791 0.0818 0.5390 70 R 0.6480 0.0423 0.3097 71 V 0.8428 0.0160 0.1411 72 E 0.8956 0.0122 0.0922 73 V 0.8923 0.0116 0.0961 74 K 0.8763 0.0087 0.1150 75 M 0.6783 0.0142 0.3075 76 N 0.2410 0.0257 0.7333 77 E 0.0453 0.1021 0.8525 78 G 0.0455 0.0691 0.8853 79 D 0.2366 0.0387 0.7246 80 E 0.7018 0.0183 0.2799 81 A 0.8934 0.0053 0.1013 82 L 0.9175 0.0050 0.0776 83 I 0.9292 0.0053 0.0656 84 I 0.9252 0.0053 0.0694 85 M 0.9161 0.0071 0.0769 86 I 0.8428 0.0262 0.1310 87 S 0.7220 0.0717 0.2063 88 Q 0.5522 0.1678 0.2800 89 R 0.4033 0.2711 0.3257 90 L 0.2105 0.4384 0.3511 91 E 0.0943 0.4902 0.4156 92 E 0.0753 0.2903 0.6344 93 G 0.0632 0.0914 0.8455 94 K 0.1922 0.0689 0.7389 95 V 0.4251 0.0559 0.5190 96 L 0.2484 0.0617 0.6899 97 S 0.1233 0.0427 0.8340 98 D 0.0086 0.9035 0.0879 99 K 0.0062 0.9356 0.0582 100 E 0.0071 0.9391 0.0538 101 I 0.0063 0.9470 0.0467 102 K 0.0103 0.9388 0.0509 103 D 0.0098 0.9350 0.0551 104 M 0.0153 0.9155 0.0691 105 Y 0.0202 0.8827 0.0971 106 R 0.0187 0.7949 0.1864 107 Q 0.0384 0.3395 0.6222 108 G 0.0440 0.0404 0.9156 109 K 0.1928 0.0252 0.7820 110 I 0.6163 0.0073 0.3765 111 S 0.7853 0.0074 0.2073 112 F 0.8753 0.0060 0.1187 113 Y 0.8693 0.0060 0.1247 114 E 0.7978 0.0046 0.1976 115 V 0.5066 0.0100 0.4834 116 W 0.0692 0.0161 0.9148