# This file is the result of combining several RDB files, specifically # T0139.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0139.t2k.stride-ebghtl.rdb (weight 1.24869) # T0139.t2k.str.rdb (weight 1.53983) # T0139.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 T0139.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0139 # 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 T0139.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 3 # # ============================================ # Comments from T0139.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0139 # 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 T0139.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 3 # # ============================================ # Comments from T0139.t2k.str.rdb # ============================================ # TARGET T0139 # 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 T0139.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 3 # # ============================================ # Comments from T0139.t2k.alpha.rdb # ============================================ # TARGET T0139 # 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 T0139.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 3 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.1202 0.0620 0.8178 2 G 0.1476 0.0737 0.7787 3 I 0.1902 0.1510 0.6589 4 S 0.1252 0.2055 0.6693 5 R 0.1042 0.4128 0.4830 6 E 0.1249 0.4949 0.3802 7 T 0.1150 0.5498 0.3352 8 S 0.0744 0.6876 0.2380 9 S 0.0472 0.7578 0.1950 10 D 0.0265 0.8674 0.1061 11 V 0.0291 0.8761 0.0947 12 A 0.0355 0.8676 0.0969 13 L 0.0399 0.8647 0.0954 14 A 0.0220 0.8865 0.0915 15 S 0.0153 0.8855 0.0992 16 H 0.0153 0.8902 0.0945 17 I 0.0202 0.9031 0.0767 18 L 0.0177 0.9079 0.0744 19 T 0.0170 0.8958 0.0872 20 A 0.0184 0.8634 0.1182 21 L 0.0454 0.7720 0.1826 22 R 0.0502 0.6788 0.2710 23 E 0.0778 0.4038 0.5184 24 K 0.0939 0.1566 0.7495 25 Q 0.0910 0.0851 0.8239 26 A 0.0931 0.0691 0.8378 27 P 0.0966 0.0892 0.8142 28 E 0.2419 0.1579 0.6003 29 L 0.3369 0.1266 0.5365 30 S 0.3822 0.0808 0.5370 31 L 0.2580 0.1356 0.6064 32 S 0.1922 0.1364 0.6714 33 S 0.1596 0.3435 0.4969 34 Q 0.1551 0.3254 0.5196 35 D 0.1870 0.2984 0.5146 36 L 0.1170 0.5703 0.3127 37 E 0.0989 0.5770 0.3241 38 L 0.1090 0.5473 0.3437 39 V 0.1280 0.3655 0.5065 40 T 0.1227 0.2694 0.6078 41 K 0.0557 0.3513 0.5930 42 E 0.0552 0.2964 0.6484 43 D 0.0975 0.0854 0.8170 44 P 0.0143 0.6207 0.3650 45 K 0.0210 0.6828 0.2962 46 A 0.0614 0.7203 0.2183 47 L 0.1072 0.7378 0.1551 48 A 0.2004 0.6734 0.1262 49 V 0.2824 0.5871 0.1305 50 A 0.2729 0.5571 0.1700 51 L 0.2427 0.4497 0.3076 52 N 0.2055 0.3426 0.4519 53 W 0.1649 0.3320 0.5031 54 D 0.1909 0.2792 0.5298 55 I 0.1067 0.5042 0.3890 56 K 0.0745 0.4907 0.4348 57 K 0.0660 0.5425 0.3916 58 T 0.0598 0.6264 0.3138 59 E 0.0410 0.7555 0.2035 60 T 0.0433 0.7874 0.1693 61 V 0.0243 0.8655 0.1101 62 Q 0.0159 0.8840 0.1001 63 E 0.0123 0.8896 0.0981 64 A 0.0124 0.8587 0.1289 65 C 0.0149 0.8243 0.1608 66 E 0.0115 0.8652 0.1233 67 R 0.0129 0.8792 0.1079 68 E 0.0183 0.8905 0.0913 69 L 0.0241 0.8959 0.0801 70 A 0.0307 0.8874 0.0819 71 L 0.0376 0.8676 0.0948 72 R 0.0431 0.8528 0.1041 73 L 0.0281 0.8724 0.0994 74 Q 0.0338 0.8416 0.1246 75 Q 0.0381 0.8179 0.1440 76 T 0.0687 0.7449 0.1864 77 Q 0.0619 0.7210 0.2171 78 S 0.0733 0.6602 0.2665 79 L 0.0609 0.6448 0.2944 80 H 0.0685 0.5093 0.4222 81 S 0.0720 0.3580 0.5699 82 L 0.0691 0.2120 0.7189 83 R 0.0410 0.0457 0.9132