# This file is the result of combining several RDB files, specifically # T0181.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0181.t2k.stride-ebghtl.rdb (weight 1.24869) # T0181.t2k.str.rdb (weight 1.53983) # T0181.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 T0181.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0181 # 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 T0181.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 2 # # ============================================ # Comments from T0181.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0181 # 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 T0181.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 2 # # ============================================ # Comments from T0181.t2k.str.rdb # ============================================ # TARGET T0181 # 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 T0181.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 2 # # ============================================ # Comments from T0181.t2k.alpha.rdb # ============================================ # TARGET T0181 # 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 T0181.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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0627 0.0369 0.9005 2 S 0.1567 0.0651 0.7781 3 T 0.2543 0.0660 0.6798 4 V 0.3784 0.0641 0.5575 5 T 0.5449 0.0483 0.4067 6 K 0.7053 0.0441 0.2506 7 Y 0.7624 0.0307 0.2069 8 F 0.7657 0.0302 0.2041 9 Y 0.7057 0.0253 0.2690 10 K 0.4485 0.0301 0.5214 11 G 0.1783 0.0868 0.7350 12 E 0.0755 0.1239 0.8007 13 N 0.1200 0.0730 0.8070 14 T 0.3629 0.0225 0.6145 15 D 0.6238 0.0233 0.3529 16 L 0.8879 0.0057 0.1064 17 I 0.9123 0.0060 0.0817 18 V 0.9059 0.0078 0.0863 19 F 0.8652 0.0122 0.1227 20 A 0.6553 0.0293 0.3154 21 A 0.2565 0.0587 0.6848 22 S 0.1022 0.0483 0.8495 23 E 0.0752 0.1991 0.7258 24 E 0.0546 0.5097 0.4357 25 L 0.0858 0.6153 0.2990 26 V 0.0709 0.7375 0.1915 27 D 0.0596 0.7704 0.1699 28 E 0.0651 0.7592 0.1757 29 Y 0.0794 0.6912 0.2294 30 L 0.0945 0.5248 0.3807 31 K 0.0604 0.3598 0.5798 32 N 0.0724 0.0911 0.8365 33 P 0.0285 0.2159 0.7557 34 S 0.0463 0.2210 0.7327 35 I 0.0630 0.2963 0.6407 36 G 0.0566 0.3027 0.6407 37 K 0.0722 0.4233 0.5045 38 L 0.0483 0.7105 0.2412 39 S 0.0634 0.7678 0.1689 40 E 0.1202 0.7136 0.1662 41 V 0.1830 0.6584 0.1587 42 V 0.3208 0.4960 0.1831 43 E 0.3977 0.4059 0.1963 44 L 0.4460 0.3305 0.2235 45 F 0.6521 0.1291 0.2189 46 E 0.7348 0.0818 0.1834 47 V 0.7599 0.0548 0.1853 48 F 0.7477 0.0288 0.2235 49 T 0.5438 0.0183 0.4379 50 P 0.2530 0.0701 0.6769 51 Q 0.0942 0.0922 0.8136 52 D 0.0645 0.0746 0.8609 53 G 0.0569 0.0827 0.8604 54 R 0.1158 0.0717 0.8126 55 G 0.0995 0.0759 0.8247 56 A 0.1248 0.1098 0.7654 57 E 0.1815 0.1677 0.6508 58 G 0.1839 0.2265 0.5896 59 E 0.2644 0.2731 0.4625 60 L 0.3213 0.3491 0.3296 61 G 0.3031 0.3727 0.3241 62 A 0.2307 0.4465 0.3228 63 A 0.1638 0.4867 0.3495 64 S 0.1420 0.4797 0.3784 65 K 0.0300 0.8321 0.1379 66 A 0.0348 0.8352 0.1300 67 Q 0.0323 0.8565 0.1112 68 V 0.0421 0.8402 0.1177 69 E 0.0378 0.8150 0.1472 70 N 0.0420 0.7411 0.2169 71 E 0.0314 0.6611 0.3075 72 F 0.0536 0.4455 0.5009 73 G 0.0499 0.2105 0.7395 74 K 0.0473 0.2422 0.7105 75 G 0.0599 0.2980 0.6421 76 K 0.0725 0.4082 0.5193 77 K 0.1134 0.4472 0.4394 78 I 0.0268 0.8218 0.1514 79 E 0.0129 0.8952 0.0919 80 E 0.0133 0.9143 0.0725 81 V 0.0119 0.9303 0.0578 82 I 0.0109 0.9384 0.0507 83 D 0.0121 0.9418 0.0462 84 L 0.0099 0.9424 0.0477 85 I 0.0140 0.9362 0.0499 86 L 0.0163 0.9068 0.0770 87 R 0.0209 0.7817 0.1975 88 N 0.0409 0.3505 0.6087 89 G 0.0483 0.0558 0.8959 90 K 0.0971 0.0338 0.8691 91 P 0.1319 0.0708 0.7973 92 N 0.0912 0.0894 0.8194 93 S 0.1349 0.1025 0.7627 94 T 0.1983 0.1217 0.6800 95 T 0.2586 0.1735 0.5679 96 S 0.2559 0.2128 0.5313 97 S 0.3068 0.2049 0.4883 98 L 0.3897 0.1858 0.4245 99 K 0.4114 0.1431 0.4455 100 T 0.3195 0.1388 0.5418 101 K 0.1497 0.1414 0.7089 102 G 0.0965 0.0995 0.8040 103 G 0.1073 0.0898 0.8029 104 N 0.1452 0.1291 0.7257 105 A 0.1410 0.2056 0.6534 106 G 0.1408 0.2039 0.6553 107 T 0.2105 0.2294 0.5601 108 K 0.2615 0.2400 0.4985 109 A 0.2483 0.2163 0.5354 110 Y 0.1402 0.1394 0.7203 111 N 0.0483 0.0319 0.9198