# This file is the result of combining several RDB files, specifically # T0214.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0214.t2k.stride-ebghtl.rdb (weight 1.24869) # T0214.t2k.str2.rdb (weight 1.54758) # T0214.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 T0214.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0214 # 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 T0214.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 15 # # ============================================ # Comments from T0214.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0214 # 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 T0214.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 15 # # ============================================ # Comments from T0214.t2k.str2.rdb # ============================================ # TARGET T0214 # 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 T0214.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 15 # # ============================================ # Comments from T0214.t2k.alpha.rdb # ============================================ # TARGET T0214 # 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 T0214.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 15 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1098 0.0331 0.8571 2 E 0.3917 0.0558 0.5525 3 W 0.5660 0.0764 0.3576 4 E 0.5709 0.0956 0.3335 5 M 0.3718 0.1636 0.4646 6 G 0.2280 0.1458 0.6262 7 L 0.2130 0.1388 0.6482 8 Q 0.1645 0.1683 0.6673 9 E 0.0949 0.3341 0.5710 10 E 0.0691 0.5790 0.3520 11 F 0.0472 0.7322 0.2206 12 L 0.0612 0.8233 0.1155 13 E 0.0557 0.8619 0.0825 14 L 0.0688 0.8429 0.0883 15 I 0.0730 0.8177 0.1094 16 K 0.0809 0.7346 0.1846 17 L 0.0596 0.3585 0.5818 18 R 0.0393 0.0398 0.9209 19 K 0.1332 0.0159 0.8509 20 K 0.4776 0.0086 0.5137 21 K 0.7323 0.0060 0.2616 22 I 0.8520 0.0058 0.1421 23 E 0.8946 0.0044 0.1010 24 G 0.8650 0.0075 0.1275 25 R 0.8193 0.0078 0.1728 26 L 0.5597 0.0368 0.4035 27 Y 0.1909 0.0794 0.7297 28 D 0.0704 0.3680 0.5616 29 E 0.0268 0.5966 0.3766 30 K 0.0244 0.6286 0.3470 31 R 0.0398 0.6769 0.2833 32 R 0.0532 0.5768 0.3700 33 Q 0.1319 0.3825 0.4856 34 I 0.2046 0.0703 0.7251 35 K 0.0893 0.0350 0.8757 36 P 0.0333 0.0933 0.8734 37 G 0.0326 0.0448 0.9225 38 D 0.2573 0.0211 0.7216 39 V 0.7762 0.0106 0.2132 40 I 0.8856 0.0062 0.1082 41 S 0.8900 0.0069 0.1031 42 F 0.7817 0.0133 0.2051 43 E 0.4292 0.0417 0.5291 44 G 0.0850 0.0414 0.8736 45 G 0.1421 0.0587 0.7992 46 K 0.5431 0.0205 0.4363 47 L 0.7919 0.0058 0.2022 48 K 0.8820 0.0046 0.1135 49 V 0.9068 0.0037 0.0895 50 R 0.9092 0.0047 0.0861 51 V 0.9054 0.0039 0.0908 52 K 0.8446 0.0164 0.1391 53 A 0.8830 0.0060 0.1111 54 I 0.8080 0.0285 0.1635 55 R 0.8056 0.0330 0.1614 56 V 0.7354 0.0550 0.2096 57 Y 0.5478 0.0894 0.3629 58 N 0.3701 0.1386 0.4913 59 S 0.2428 0.2004 0.5568 60 F 0.0108 0.8932 0.0959 61 R 0.0049 0.9426 0.0524 62 E 0.0052 0.9467 0.0481 63 M 0.0050 0.9430 0.0520 64 L 0.0079 0.9080 0.0841 65 E 0.0094 0.8503 0.1403 66 K 0.0172 0.7566 0.2262 67 E 0.0671 0.5432 0.3897 68 G 0.0686 0.3192 0.6122 69 L 0.0446 0.5067 0.4486 70 E 0.0703 0.5495 0.3803 71 N 0.1220 0.4746 0.4034 72 V 0.2041 0.2156 0.5803 73 L 0.1034 0.0712 0.8254 74 P 0.0437 0.1227 0.8336 75 G 0.0328 0.0771 0.8902 76 V 0.0717 0.0528 0.8754 77 K 0.0867 0.0763 0.8370 78 S 0.1502 0.1410 0.7089 79 I 0.0053 0.9264 0.0683 80 E 0.0047 0.9495 0.0458 81 E 0.0047 0.9508 0.0445 82 G 0.0047 0.9495 0.0458 83 I 0.0053 0.9459 0.0488 84 Q 0.0057 0.9401 0.0542 85 V 0.0056 0.9325 0.0619 86 Y 0.0092 0.9107 0.0802 87 R 0.0137 0.8502 0.1361 88 R 0.0215 0.7264 0.2521 89 F 0.0390 0.4976 0.4634 90 Y 0.1003 0.1374 0.7623 91 D 0.0557 0.0811 0.8632 92 E 0.0069 0.8982 0.0949 93 E 0.0069 0.9081 0.0850 94 K 0.0072 0.9096 0.0832 95 E 0.0346 0.8355 0.1298 96 K 0.0660 0.7381 0.1959 97 K 0.0720 0.5138 0.4141 98 Y 0.1194 0.1798 0.7008 99 G 0.1872 0.0377 0.7751 100 V 0.4775 0.0081 0.5144 101 V 0.7568 0.0072 0.2360 102 A 0.8959 0.0044 0.0997 103 I 0.9119 0.0049 0.0833 104 E 0.9147 0.0039 0.0814 105 I 0.8855 0.0064 0.1081 106 E 0.8239 0.0085 0.1676 107 P 0.7168 0.0259 0.2573 108 L 0.3122 0.0612 0.6266 109 E 0.1819 0.0512 0.7669 110 Y 0.0422 0.0340 0.9238