# This file is the result of combining several RDB files, specifically # T0263.t04.dssp-ebghstl.rdb (weight 1.53986) # T0263.t04.stride-ebghtl.rdb (weight 1.24869) # T0263.t04.str2.rdb (weight 1.54758) # T0263.t04.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 T0263.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0263 # Using neural net t04-2621-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 T0263.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 14.1225 # # ============================================ # Comments from T0263.t04.stride-ebghtl.rdb # ============================================ # TARGET T0263 # 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 T0263.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 14.1225 # # ============================================ # Comments from T0263.t04.str2.rdb # ============================================ # TARGET T0263 # 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 T0263.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 14.1225 # # ============================================ # Comments from T0263.t04.alpha.rdb # ============================================ # TARGET T0263 # 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 T0263.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 14.1225 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1051 0.0658 0.8291 2 A 0.2411 0.0521 0.7068 3 T 0.5073 0.0400 0.4527 4 L 0.8477 0.0200 0.1322 5 L 0.8929 0.0157 0.0915 6 Q 0.9108 0.0128 0.0764 7 L 0.8754 0.0177 0.1069 8 H 0.7636 0.0204 0.2161 9 F 0.6147 0.0194 0.3659 10 A 0.3781 0.0350 0.5868 11 F 0.1718 0.0560 0.7722 12 N 0.0835 0.0546 0.8619 13 G 0.0565 0.0315 0.9120 14 P 0.0704 0.1345 0.7951 15 F 0.0707 0.2949 0.6345 16 G 0.0150 0.8005 0.1844 17 D 0.0048 0.9492 0.0460 18 A 0.0048 0.9540 0.0412 19 M 0.0049 0.9498 0.0453 20 A 0.0049 0.9480 0.0471 21 E 0.0054 0.9091 0.0855 22 Q 0.0061 0.8662 0.1277 23 L 0.0083 0.8505 0.1412 24 K 0.0064 0.8813 0.1124 25 P 0.0054 0.8907 0.1039 26 L 0.0067 0.8904 0.1029 27 A 0.0072 0.9223 0.0706 28 E 0.0054 0.9185 0.0760 29 S 0.0063 0.8899 0.1038 30 I 0.0138 0.8425 0.1438 31 N 0.0165 0.6339 0.3496 32 Q 0.0377 0.3780 0.5842 33 E 0.0588 0.1013 0.8399 34 P 0.0311 0.1552 0.8137 35 G 0.0664 0.0820 0.8515 36 F 0.3346 0.0685 0.5968 37 L 0.6113 0.0354 0.3533 38 W 0.8277 0.0168 0.1555 39 K 0.8940 0.0095 0.0965 40 V 0.8945 0.0092 0.0963 41 W 0.8724 0.0137 0.1139 42 T 0.8456 0.0105 0.1439 43 E 0.7746 0.0264 0.1991 44 S 0.4072 0.0142 0.5786 45 E 0.0460 0.1444 0.8096 46 K 0.0295 0.1067 0.8639 47 N 0.0738 0.0517 0.8745 48 H 0.1484 0.0445 0.8071 49 E 0.5860 0.0391 0.3749 50 A 0.6873 0.0296 0.2831 51 G 0.6195 0.0272 0.3532 52 G 0.7873 0.0122 0.2004 53 I 0.8757 0.0077 0.1166 54 Y 0.8943 0.0071 0.0986 55 L 0.8642 0.0128 0.1230 56 F 0.6521 0.0308 0.3171 57 T 0.2406 0.0511 0.7083 58 D 0.1169 0.0363 0.8468 59 E 0.0058 0.9298 0.0644 60 K 0.0052 0.9493 0.0455 61 S 0.0052 0.9465 0.0483 62 A 0.0051 0.9503 0.0447 63 L 0.0048 0.9487 0.0465 64 A 0.0050 0.9277 0.0673 65 Y 0.0055 0.9020 0.0925 66 L 0.0072 0.8983 0.0944 67 E 0.0055 0.9031 0.0914 68 K 0.0056 0.9028 0.0916 69 H 0.0060 0.9100 0.0839 70 T 0.0054 0.9395 0.0551 71 A 0.0050 0.9494 0.0456 72 R 0.0050 0.9510 0.0440 73 L 0.0052 0.9428 0.0521 74 K 0.0062 0.9238 0.0701 75 N 0.0093 0.8062 0.1844 76 L 0.0378 0.4263 0.5359 77 G 0.0465 0.0710 0.8825 78 V 0.0867 0.0642 0.8490 79 E 0.1961 0.1002 0.7037 80 E 0.4281 0.0876 0.4843 81 V 0.7332 0.0226 0.2442 82 V 0.8807 0.0069 0.1123 83 A 0.8791 0.0056 0.1152 84 K 0.8501 0.0081 0.1418 85 V 0.8678 0.0096 0.1226 86 F 0.8086 0.0142 0.1772 87 D 0.7319 0.0137 0.2544 88 V 0.3493 0.0873 0.5635 89 N 0.1538 0.0990 0.7471 90 E 0.1483 0.0871 0.7646 91 P 0.1986 0.1757 0.6257 92 L 0.1317 0.4656 0.4027 93 S 0.0825 0.5400 0.3775 94 Q 0.1293 0.5190 0.3516 95 I 0.1929 0.3479 0.4593 96 N 0.1311 0.2280 0.6409 97 Q 0.1136 0.2113 0.6750 98 A 0.1659 0.1363 0.6978 99 K 0.2193 0.1002 0.6805 100 L 0.1172 0.0441 0.8387 101 A 0.0627 0.0269 0.9104