# This file is the result of combining several RDB files, specifically # T0230.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0230.t2k.stride-ebghtl.rdb (weight 1.24869) # T0230.t2k.str2.rdb (weight 1.54758) # T0230.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 T0230.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0230 # 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 T0230.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 175 # # ============================================ # Comments from T0230.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0230 # 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 T0230.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 175 # # ============================================ # Comments from T0230.t2k.str2.rdb # ============================================ # TARGET T0230 # 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 T0230.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 175 # # ============================================ # Comments from T0230.t2k.alpha.rdb # ============================================ # TARGET T0230 # 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 T0230.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 175 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0624 0.0341 0.9035 2 P 0.0757 0.0726 0.8516 3 M 0.0529 0.2329 0.7142 4 S 0.0415 0.2603 0.6982 5 K 0.0474 0.2712 0.6815 6 K 0.0453 0.4683 0.4864 7 V 0.0530 0.4955 0.4515 8 T 0.0677 0.5562 0.3760 9 K 0.0053 0.9426 0.0521 10 E 0.0049 0.9561 0.0390 11 D 0.0047 0.9583 0.0370 12 V 0.0047 0.9591 0.0362 13 L 0.0047 0.9579 0.0374 14 N 0.0047 0.9542 0.0410 15 A 0.0058 0.9296 0.0645 16 L 0.0302 0.8523 0.1176 17 K 0.0114 0.7699 0.2188 18 N 0.0265 0.6172 0.3563 19 V 0.0900 0.3320 0.5780 20 I 0.2090 0.1082 0.6828 21 D 0.1172 0.0442 0.8385 22 F 0.0160 0.2437 0.7403 23 E 0.0204 0.1523 0.8273 24 L 0.0728 0.1242 0.8030 25 G 0.0859 0.0768 0.8372 26 L 0.2086 0.0661 0.7253 27 D 0.3284 0.0606 0.6110 28 V 0.4946 0.2177 0.2877 29 V 0.5511 0.2142 0.2347 30 S 0.5649 0.1979 0.2373 31 L 0.3870 0.1810 0.4320 32 G 0.3563 0.0964 0.5473 33 L 0.6042 0.0728 0.3230 34 V 0.7749 0.0268 0.1983 35 Y 0.7833 0.0406 0.1761 36 D 0.8258 0.0148 0.1594 37 I 0.8841 0.0053 0.1106 38 Q 0.9029 0.0040 0.0930 39 I 0.8823 0.0063 0.1114 40 D 0.5275 0.0178 0.4547 41 D 0.0620 0.0644 0.8736 42 Q 0.0334 0.0474 0.9191 43 N 0.1005 0.0406 0.8589 44 N 0.6284 0.0054 0.3661 45 V 0.9057 0.0033 0.0911 46 K 0.9302 0.0031 0.0667 47 V 0.9289 0.0034 0.0677 48 L 0.9266 0.0033 0.0701 49 M 0.9148 0.0042 0.0810 50 T 0.8426 0.0052 0.1521 51 M 0.6758 0.0080 0.3162 52 T 0.2246 0.0377 0.7377 53 T 0.0883 0.0444 0.8673 54 P 0.0278 0.1483 0.8239 55 M 0.0382 0.1445 0.8173 56 C 0.0552 0.1612 0.7836 57 P 0.0519 0.2960 0.6521 58 L 0.0262 0.5783 0.3954 59 A 0.0089 0.8359 0.1553 60 G 0.0064 0.9077 0.0860 61 M 0.0063 0.9134 0.0803 62 I 0.0057 0.9295 0.0648 63 L 0.0048 0.9506 0.0446 64 S 0.0048 0.9547 0.0405 65 D 0.0047 0.9567 0.0385 66 A 0.0047 0.9577 0.0376 67 E 0.0047 0.9573 0.0380 68 E 0.0047 0.9536 0.0417 69 A 0.0049 0.9375 0.0576 70 I 0.0065 0.8993 0.0942 71 K 0.0071 0.7767 0.2161 72 K 0.0194 0.5555 0.4250 73 I 0.0675 0.1006 0.8319 74 E 0.0264 0.1366 0.8370 75 G 0.0444 0.0766 0.8789 76 V 0.1946 0.0472 0.7582 77 N 0.3744 0.0581 0.5675 78 N 0.7070 0.0199 0.2731 79 V 0.8172 0.0097 0.1732 80 E 0.8993 0.0036 0.0971 81 V 0.9124 0.0035 0.0841 82 E 0.9196 0.0033 0.0771 83 L 0.9043 0.0039 0.0918 84 T 0.8424 0.0061 0.1515 85 F 0.5976 0.0087 0.3937 86 D 0.2249 0.0197 0.7554 87 P 0.1101 0.0281 0.8618 88 P 0.0782 0.0610 0.8608 89 W 0.1064 0.0541 0.8395 90 T 0.0928 0.0406 0.8666 91 P 0.0413 0.4687 0.4899 92 E 0.0322 0.4928 0.4750 93 R 0.0732 0.4330 0.4938 94 M 0.1864 0.1124 0.7012 95 S 0.0538 0.0745 0.8718 96 P 0.0048 0.9532 0.0420 97 E 0.0047 0.9586 0.0367 98 L 0.0047 0.9594 0.0359 99 R 0.0047 0.9569 0.0383 100 E 0.0049 0.9400 0.0551 101 K 0.0059 0.8672 0.1268 102 F 0.0448 0.4859 0.4694 103 G 0.0501 0.1017 0.8482 104 V 0.0543 0.0233 0.9223