# This file is the result of combining several RDB files, specifically # YGR022C.t2k.dssp-ebghstl.rdb (weight 1.53986) # YGR022C.t2k.stride-ebghtl.rdb (weight 1.24869) # YGR022C.t2k.str2.rdb (weight 1.54758) # YGR022C.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 YGR022C.t2k.dssp-ebghstl.rdb # ============================================ # TARGET YGR022C # 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 YGR022C.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 1 # # ============================================ # Comments from YGR022C.t2k.stride-ebghtl.rdb # ============================================ # TARGET YGR022C # 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 YGR022C.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 1 # # ============================================ # Comments from YGR022C.t2k.str2.rdb # ============================================ # TARGET YGR022C # 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 YGR022C.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 1 # # ============================================ # Comments from YGR022C.t2k.alpha.rdb # ============================================ # TARGET YGR022C # 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 YGR022C.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0576 0.0659 0.8765 2 D 0.0922 0.1515 0.7563 3 E 0.0576 0.4234 0.5191 4 E 0.0560 0.4648 0.4792 5 E 0.0668 0.4417 0.4915 6 S 0.0758 0.3681 0.5561 7 S 0.0675 0.3484 0.5841 8 E 0.0585 0.3835 0.5580 9 D 0.0532 0.3247 0.6221 10 N 0.0736 0.2671 0.6593 11 V 0.0809 0.3479 0.5712 12 D 0.0859 0.3572 0.5570 13 E 0.0857 0.4748 0.4396 14 R 0.1236 0.4323 0.4441 15 V 0.1581 0.3560 0.4858 16 S 0.1412 0.2839 0.5749 17 S 0.0725 0.5344 0.3930 18 E 0.0531 0.6604 0.2865 19 E 0.0613 0.6521 0.2866 20 L 0.0811 0.5569 0.3619 21 C 0.0854 0.3901 0.5245 22 G 0.0708 0.2509 0.6783 23 K 0.1238 0.2623 0.6139 24 E 0.2284 0.2614 0.5103 25 V 0.1983 0.2680 0.5338 26 K 0.1588 0.2811 0.5600 27 D 0.1478 0.3172 0.5350 28 T 0.0981 0.4982 0.4037 29 E 0.1227 0.5554 0.3219 30 A 0.1452 0.5790 0.2757 31 I 0.1586 0.5574 0.2840 32 L 0.1439 0.4620 0.3941 33 G 0.1240 0.3231 0.5529 34 V 0.1110 0.4701 0.4189 35 D 0.1061 0.5542 0.3396 36 K 0.0798 0.7213 0.1990 37 L 0.0953 0.7786 0.1261 38 A 0.1347 0.7552 0.1101 39 L 0.2104 0.6803 0.1092 40 L 0.2574 0.6188 0.1237 41 V 0.3327 0.5266 0.1407 42 A 0.3073 0.5111 0.1815 43 S 0.3344 0.4342 0.2314 44 V 0.3580 0.3770 0.2650 45 L 0.4101 0.2525 0.3375 46 D 0.3660 0.1532 0.4808 47 V 0.1746 0.2169 0.6085 48 N 0.1139 0.1623 0.7238 49 D 0.0700 0.2685 0.6616 50 S 0.0632 0.4037 0.5331 51 T 0.0728 0.4700 0.4573 52 A 0.0642 0.5567 0.3791 53 E 0.0607 0.6481 0.2912 54 S 0.0642 0.6757 0.2601 55 E 0.0760 0.6845 0.2395 56 V 0.0940 0.6519 0.2541 57 M 0.0951 0.6214 0.2835 58 E 0.0784 0.5294 0.3921 59 G 0.0918 0.3517 0.5565 60 A 0.2133 0.3277 0.4590 61 V 0.4263 0.2795 0.2942 62 L 0.4971 0.2429 0.2600 63 D 0.5689 0.2131 0.2180 64 V 0.6919 0.1806 0.1274 65 V 0.7209 0.1666 0.1124 66 L 0.6996 0.1711 0.1292 67 L 0.6088 0.1663 0.2250 68 A 0.3213 0.1761 0.5026 69 G 0.1703 0.1032 0.7266 70 T 0.1567 0.1242 0.7192 71 N 0.1429 0.1778 0.6792 72 S 0.1393 0.2733 0.5874 73 C 0.1684 0.2994 0.5321 74 E 0.1935 0.3348 0.4718 75 R 0.2574 0.3203 0.4223 76 T 0.2468 0.2979 0.4553 77 L 0.2335 0.2643 0.5023 78 S 0.1612 0.2714 0.5674 79 G 0.1201 0.3146 0.5654 80 S 0.2006 0.3522 0.4472 81 V 0.3027 0.4163 0.2810 82 V 0.2784 0.4519 0.2697 83 N 0.2939 0.4304 0.2757 84 A 0.2539 0.5456 0.2006 85 M 0.3229 0.5055 0.1716 86 R 0.4534 0.4095 0.1370 87 I 0.5553 0.3407 0.1040 88 V 0.5768 0.3148 0.1084 89 L 0.5361 0.3236 0.1404 90 H 0.4680 0.2973 0.2348 91 I 0.1765 0.5404 0.2831 92 D 0.0984 0.5599 0.3417 93 R 0.0596 0.6488 0.2916 94 L 0.0581 0.7005 0.2415 95 E 0.0540 0.7382 0.2078 96 A 0.0471 0.7991 0.1539 97 E 0.0660 0.8062 0.1277 98 L 0.1132 0.7841 0.1027 99 F 0.1504 0.7465 0.1031 100 F 0.1638 0.7348 0.1014 101 L 0.1526 0.7299 0.1175 102 V 0.1338 0.6912 0.1750 103 G 0.1591 0.5851 0.2558 104 L 0.2006 0.5378 0.2615 105 Q 0.2285 0.4894 0.2821 106 L 0.2313 0.3931 0.3756 107 A 0.2101 0.2529 0.5371 108 I 0.1006 0.0936 0.8058 109 P 0.0503 0.0253 0.9244