# This file is the result of combining several RDB files, specifically # T0408.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0408.t2k.stride-ebghtl.rdb (weight 1.24869) # T0408.t2k.str2.rdb (weight 1.54758) # T0408.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 T0408.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0408 # 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 T0408.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 348 # # ============================================ # Comments from T0408.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0408 # 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 T0408.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 348 # # ============================================ # Comments from T0408.t2k.str2.rdb # ============================================ # TARGET T0408 # 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 T0408.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 348 # # ============================================ # Comments from T0408.t2k.alpha.rdb # ============================================ # TARGET T0408 # 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 T0408.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 348 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0599 0.0541 0.8860 2 K 0.1407 0.1122 0.7471 3 N 0.1581 0.1495 0.6924 4 E 0.0890 0.3603 0.5506 5 V 0.1119 0.3813 0.5068 6 F 0.1330 0.3827 0.4843 7 F 0.0768 0.4024 0.5208 8 G 0.0109 0.8393 0.1498 9 E 0.0074 0.9065 0.0861 10 G 0.0060 0.9218 0.0722 11 M 0.0064 0.9217 0.0720 12 K 0.0065 0.9069 0.0866 13 V 0.0070 0.8846 0.1084 14 V 0.0091 0.8520 0.1389 15 K 0.0082 0.8099 0.1819 16 E 0.0089 0.7271 0.2640 17 K 0.0166 0.6409 0.3425 18 Y 0.0533 0.3322 0.6145 19 P 0.0069 0.8078 0.1853 20 D 0.0055 0.8784 0.1161 21 L 0.0052 0.9288 0.0659 22 Y 0.0050 0.9497 0.0452 23 D 0.0054 0.9533 0.0413 24 I 0.0051 0.9530 0.0419 25 I 0.0052 0.9519 0.0429 26 V 0.0056 0.9468 0.0475 27 K 0.0067 0.9215 0.0718 28 L 0.0101 0.8708 0.1191 29 N 0.0192 0.7677 0.2131 30 D 0.0219 0.6979 0.2803 31 T 0.0363 0.7042 0.2595 32 V 0.0771 0.6140 0.3089 33 F 0.0942 0.4575 0.4483 34 T 0.0723 0.2727 0.6550 35 G 0.0524 0.1893 0.7584 36 K 0.0338 0.1660 0.8002 37 T 0.0589 0.1540 0.7871 38 L 0.0829 0.0809 0.8362 39 D 0.0652 0.0566 0.8782 40 Y 0.0073 0.8505 0.1423 41 K 0.0059 0.8970 0.0971 42 T 0.0056 0.9408 0.0536 43 Q 0.0047 0.9530 0.0423 44 K 0.0047 0.9570 0.0383 45 L 0.0047 0.9599 0.0354 46 I 0.0047 0.9608 0.0346 47 A 0.0047 0.9608 0.0345 48 I 0.0046 0.9612 0.0341 49 G 0.0046 0.9613 0.0340 50 I 0.0047 0.9610 0.0343 51 V 0.0047 0.9603 0.0350 52 A 0.0049 0.9517 0.0434 53 S 0.0057 0.9206 0.0738 54 R 0.0353 0.5960 0.3687 55 C 0.0330 0.1878 0.7792 56 D 0.0701 0.0816 0.8483 57 E 0.0139 0.7835 0.2026 58 V 0.0076 0.8779 0.1145 59 A 0.0055 0.9272 0.0673 60 I 0.0052 0.9446 0.0502 61 E 0.0048 0.9521 0.0432 62 K 0.0048 0.9562 0.0390 63 Q 0.0047 0.9586 0.0367 64 M 0.0047 0.9585 0.0368 65 K 0.0047 0.9596 0.0357 66 S 0.0047 0.9599 0.0354 67 A 0.0047 0.9590 0.0363 68 M 0.0048 0.9564 0.0387 69 K 0.0051 0.9475 0.0474 70 E 0.0072 0.8604 0.1324 71 L 0.0421 0.2702 0.6877 72 G 0.0347 0.0230 0.9423 73 I 0.0604 0.0092 0.9304 74 T 0.0589 0.0109 0.9302 75 K 0.0052 0.9184 0.0764 76 E 0.0048 0.9427 0.0525 77 E 0.0048 0.9555 0.0398 78 I 0.0047 0.9600 0.0354 79 A 0.0047 0.9599 0.0354 80 D 0.0047 0.9593 0.0361 81 V 0.0047 0.9589 0.0364 82 L 0.0047 0.9597 0.0356 83 R 0.0047 0.9580 0.0373 84 V 0.0048 0.9577 0.0375 85 V 0.0047 0.9591 0.0362 86 L 0.0048 0.9547 0.0405 87 L 0.0053 0.9409 0.0538 88 T 0.0093 0.8795 0.1112 89 S 0.0157 0.7492 0.2352 90 G 0.0185 0.5814 0.4000 91 M 0.0175 0.7432 0.2393 92 P 0.0061 0.9437 0.0502 93 A 0.0049 0.9526 0.0425 94 F 0.0048 0.9569 0.0384 95 T 0.0048 0.9575 0.0376 96 K 0.0048 0.9563 0.0389 97 A 0.0047 0.9564 0.0388 98 M 0.0047 0.9552 0.0401 99 K 0.0049 0.9485 0.0467 100 I 0.0049 0.9364 0.0587 101 L 0.0060 0.8974 0.0966 102 E 0.0066 0.7615 0.2319 103 K 0.0124 0.5538 0.4338 104 L 0.0336 0.1355 0.8309