# This file is the result of combining several RDB files, specifically # T0188.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0188.t2k.stride-ebghtl.rdb (weight 1.24869) # T0188.t2k.str.rdb (weight 1.53983) # T0188.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 T0188.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0188 # 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 T0188.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 38 # # ============================================ # Comments from T0188.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0188 # 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 T0188.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 38 # # ============================================ # Comments from T0188.t2k.str.rdb # ============================================ # TARGET T0188 # 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 T0188.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 38 # # ============================================ # Comments from T0188.t2k.alpha.rdb # ============================================ # TARGET T0188 # 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 T0188.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 38 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1328 0.0078 0.8594 2 I 0.6495 0.0076 0.3429 3 I 0.8614 0.0048 0.1339 4 A 0.8716 0.0053 0.1231 5 I 0.8495 0.0057 0.1447 6 P 0.7139 0.0084 0.2777 7 V 0.3593 0.0294 0.6113 8 S 0.1408 0.0578 0.8014 9 E 0.0739 0.0579 0.8682 10 N 0.0625 0.0977 0.8398 11 R 0.0815 0.1024 0.8161 12 G 0.0883 0.0720 0.8397 13 K 0.0992 0.1223 0.7786 14 D 0.0891 0.1101 0.8008 15 S 0.1687 0.1044 0.7269 16 P 0.2708 0.1368 0.5923 17 I 0.3526 0.1258 0.5217 18 S 0.2616 0.1659 0.5726 19 E 0.1543 0.3050 0.5407 20 H 0.1936 0.2644 0.5420 21 F 0.2401 0.2154 0.5445 22 G 0.2201 0.1098 0.6701 23 R 0.2161 0.0914 0.6925 24 A 0.2263 0.0323 0.7413 25 P 0.1420 0.0615 0.7964 26 Y 0.5454 0.0195 0.4351 27 F 0.8847 0.0041 0.1112 28 A 0.9214 0.0039 0.0747 29 F 0.9302 0.0033 0.0665 30 V 0.9140 0.0055 0.0805 31 K 0.8992 0.0042 0.0966 32 V 0.6844 0.0156 0.3001 33 K 0.2072 0.0375 0.7553 34 N 0.0493 0.0470 0.9037 35 N 0.0571 0.0563 0.8866 36 A 0.4981 0.0186 0.4833 37 I 0.8538 0.0040 0.1422 38 A 0.8562 0.0133 0.1305 39 D 0.8883 0.0057 0.1060 40 I 0.8391 0.0173 0.1436 41 S 0.8227 0.0183 0.1590 42 V 0.7926 0.0190 0.1884 43 E 0.6873 0.0234 0.2892 44 E 0.5001 0.0444 0.4554 45 N 0.2298 0.0404 0.7298 46 P 0.1361 0.0998 0.7641 47 L 0.0744 0.3162 0.6094 48 A 0.0593 0.3886 0.5521 49 Q 0.0596 0.3320 0.6084 50 D 0.0437 0.2701 0.6862 51 H 0.0428 0.1751 0.7821 52 V 0.0578 0.1817 0.7605 53 H 0.0739 0.1935 0.7326 54 G 0.0910 0.3439 0.5651 55 A 0.1065 0.4402 0.4533 56 V 0.0231 0.8611 0.1158 57 P 0.0116 0.9228 0.0656 58 N 0.0128 0.9326 0.0545 59 F 0.0100 0.9412 0.0488 60 V 0.0112 0.9363 0.0524 61 K 0.0099 0.9246 0.0655 62 E 0.0161 0.8466 0.1373 63 K 0.0420 0.3474 0.6106 64 G 0.0426 0.0226 0.9348 65 A 0.1149 0.0075 0.8776 66 E 0.4044 0.0296 0.5660 67 L 0.9263 0.0037 0.0700 68 V 0.9328 0.0035 0.0637 69 I 0.9261 0.0037 0.0702 70 V 0.8532 0.0142 0.1325 71 R 0.3440 0.0499 0.6061 72 G 0.1157 0.1049 0.7793 73 I 0.0963 0.1292 0.7745 74 G 0.0554 0.0730 0.8716 75 R 0.0227 0.6096 0.3678 76 R 0.0205 0.7447 0.2348 77 A 0.0060 0.9303 0.0637 78 I 0.0047 0.9506 0.0447 79 A 0.0046 0.9523 0.0431 80 A 0.0044 0.9568 0.0388 81 F 0.0045 0.9544 0.0412 82 E 0.0047 0.9448 0.0505 83 A 0.0056 0.8950 0.0994 84 M 0.0412 0.3152 0.6436 85 G 0.0416 0.0165 0.9419 86 V 0.1231 0.0077 0.8692 87 K 0.6378 0.0076 0.3546 88 V 0.8885 0.0039 0.1075 89 I 0.8869 0.0087 0.1045 90 K 0.8641 0.0054 0.1304 91 G 0.4928 0.0121 0.4951 92 A 0.1238 0.0339 0.8423 93 S 0.0538 0.0468 0.8994 94 G 0.1132 0.0386 0.8482 95 T 0.2218 0.0387 0.7395 96 V 0.0078 0.8996 0.0927 97 E 0.0044 0.9431 0.0525 98 E 0.0044 0.9530 0.0426 99 V 0.0044 0.9541 0.0415 100 V 0.0047 0.9531 0.0422 101 N 0.0050 0.9480 0.0470 102 Q 0.0046 0.9378 0.0576 103 Y 0.0058 0.9159 0.0783 104 L 0.0083 0.7893 0.2024 105 S 0.0381 0.3687 0.5931 106 G 0.0427 0.1514 0.8059 107 Q 0.1211 0.1052 0.7736 108 L 0.2064 0.1523 0.6413 109 K 0.1600 0.2174 0.6226 110 D 0.1727 0.3434 0.4839 111 S 0.1763 0.2576 0.5661 112 D 0.1952 0.1677 0.6371 113 Y 0.1518 0.1159 0.7323 114 E 0.1149 0.1403 0.7449 115 V 0.1106 0.1461 0.7434 116 H 0.0988 0.1328 0.7683 117 D 0.0839 0.1222 0.7939 118 H 0.0721 0.1280 0.7999 119 H 0.0826 0.1076 0.8098 120 H 0.0981 0.1245 0.7773 121 H 0.1087 0.1090 0.7823 122 E 0.1403 0.0954 0.7643 123 H 0.1407 0.0728 0.7865 124 H 0.0426 0.0374 0.9200