# This file is the result of combining several RDB files, specifically # T0358.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0358.t2k.stride-ebghtl.rdb (weight 1.24869) # T0358.t2k.str2.rdb (weight 1.54758) # T0358.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 T0358.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0358 # 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 T0358.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 14 # # ============================================ # Comments from T0358.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0358 # 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 T0358.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 14 # # ============================================ # Comments from T0358.t2k.str2.rdb # ============================================ # TARGET T0358 # 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 T0358.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 14 # # ============================================ # Comments from T0358.t2k.alpha.rdb # ============================================ # TARGET T0358 # 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 T0358.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 14 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0811 0.0291 0.8898 2 T 0.1780 0.0496 0.7723 3 Q 0.1888 0.1289 0.6822 4 S 0.1750 0.1961 0.6288 5 V 0.2581 0.1758 0.5661 6 L 0.2685 0.1032 0.6284 7 L 0.1227 0.0391 0.8382 8 P 0.0631 0.0804 0.8565 9 P 0.0595 0.0658 0.8747 10 G 0.0610 0.0412 0.8978 11 P 0.0897 0.0720 0.8383 12 F 0.1428 0.0928 0.7644 13 T 0.1039 0.1735 0.7226 14 R 0.0076 0.9219 0.0705 15 R 0.0058 0.9405 0.0537 16 Q 0.0049 0.9518 0.0433 17 A 0.0051 0.9560 0.0389 18 Q 0.0054 0.9565 0.0381 19 A 0.0051 0.9555 0.0394 20 V 0.0054 0.9553 0.0394 21 T 0.0079 0.9433 0.0488 22 T 0.0135 0.8979 0.0886 23 T 0.0345 0.8049 0.1606 24 Y 0.1108 0.6404 0.2488 25 S 0.1109 0.4538 0.4353 26 N 0.1832 0.2792 0.5375 27 I 0.3719 0.1876 0.4405 28 T 0.5316 0.1127 0.3557 29 L 0.4431 0.1741 0.3828 30 E 0.3508 0.1373 0.5119 31 D 0.2155 0.1045 0.6800 32 D 0.1568 0.0450 0.7982 33 Q 0.1007 0.0815 0.8178 34 G 0.1200 0.1119 0.7681 35 S 0.2491 0.0998 0.6512 36 H 0.6313 0.0404 0.3283 37 F 0.8076 0.0119 0.1805 38 R 0.8918 0.0101 0.0981 39 L 0.9185 0.0041 0.0773 40 V 0.9142 0.0044 0.0815 41 V 0.8881 0.0067 0.1052 42 R 0.8289 0.0094 0.1617 43 D 0.3433 0.0164 0.6403 44 T 0.0507 0.1130 0.8363 45 E 0.0597 0.0256 0.9147 46 G 0.1034 0.0285 0.8680 47 R 0.4220 0.0128 0.5652 48 M 0.8777 0.0043 0.1180 49 V 0.8852 0.0068 0.1080 50 W 0.9051 0.0045 0.0904 51 R 0.8381 0.0103 0.1516 52 A 0.7584 0.0157 0.2259 53 W 0.6321 0.0313 0.3366 54 N 0.4515 0.0388 0.5098 55 F 0.2047 0.0539 0.7415 56 E 0.0930 0.0483 0.8587 57 P 0.0308 0.1869 0.7823 58 D 0.0297 0.1548 0.8155 59 A 0.0513 0.3212 0.6275 60 G 0.0330 0.3914 0.5757 61 E 0.0330 0.6551 0.3119 62 G 0.0327 0.7478 0.2195 63 L 0.0250 0.8533 0.1217 64 N 0.0207 0.8848 0.0945 65 R 0.0130 0.9187 0.0683 66 Y 0.0219 0.9021 0.0760 67 I 0.0297 0.8704 0.0999 68 R 0.0337 0.8123 0.1540 69 T 0.0301 0.6729 0.2970 70 S 0.0561 0.3420 0.6020 71 G 0.0800 0.1086 0.8114 72 I 0.2377 0.1058 0.6565 73 R 0.2570 0.0941 0.6489 74 T 0.1831 0.1072 0.7097 75 D 0.1345 0.1076 0.7579 76 T 0.1031 0.1100 0.7869 77 A 0.1144 0.0785 0.8071 78 T 0.0915 0.0557 0.8528 79 R 0.0493 0.0297 0.9210