# This file is the result of combining several RDB files, specifically # T0630.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0630.t2k.stride-ebghtl.rdb (weight 1.24869) # T0630.t2k.str.rdb (weight 1.53983) # 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 T0630.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0630 # 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 T0630.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 224 # # ============================================ # Comments from T0630.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0630 # 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 T0630.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 224 # # ============================================ # Comments from T0630.t2k.str.rdb # ============================================ # TARGET T0630 # 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 T0630.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 224 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0183 0.0215 0.9602 2 R 0.0953 0.0735 0.8312 3 A 0.0888 0.1257 0.7855 4 P 0.0641 0.1552 0.7807 5 I 0.0673 0.2299 0.7028 6 P 0.0599 0.1471 0.7929 7 E 0.0991 0.0443 0.8566 8 P 0.0583 0.0112 0.9305 9 K 0.0566 0.0163 0.9270 10 P 0.0425 0.0718 0.8857 11 G 0.0342 0.0635 0.9023 12 D 0.2189 0.0325 0.7486 13 L 0.8780 0.0043 0.1177 14 I 0.9547 0.0028 0.0425 15 E 0.9534 0.0031 0.0435 16 I 0.8325 0.0049 0.1626 17 F 0.5260 0.0094 0.4646 18 R 0.2917 0.0292 0.6791 19 P 0.1557 0.0404 0.8038 20 F 0.2436 0.0614 0.6951 21 Y 0.4617 0.0323 0.5060 22 R 0.6434 0.0161 0.3405 23 H 0.8537 0.0083 0.1380 24 W 0.8957 0.0051 0.0993 25 A 0.9559 0.0032 0.0409 26 I 0.9662 0.0025 0.0313 27 Y 0.9615 0.0024 0.0361 28 V 0.8088 0.0035 0.1877 29 G 0.3512 0.0167 0.6322 30 D 0.0362 0.0308 0.9330 31 G 0.0829 0.0380 0.8791 32 Y 0.6763 0.0140 0.3097 33 V 0.9239 0.0028 0.0733 34 V 0.9478 0.0035 0.0487 35 H 0.9333 0.0035 0.0632 36 L 0.7940 0.0064 0.1996 37 A 0.5265 0.0104 0.4632 38 P 0.1927 0.0364 0.7708 39 P 0.0790 0.1036 0.8174 40 S 0.0916 0.1708 0.7377 41 E 0.1610 0.1754 0.6636 42 V 0.2878 0.1345 0.5777 43 A 0.3617 0.1223 0.5160 44 G 0.3998 0.1099 0.4903 45 A 0.4125 0.1070 0.4805 46 G 0.3652 0.1111 0.5236 47 A 0.3499 0.2391 0.4110 48 A 0.4115 0.2803 0.3082 49 S 0.4302 0.2979 0.2718 50 V 0.3923 0.3159 0.2919 51 M 0.3497 0.3177 0.3327 52 S 0.2894 0.3635 0.3472 53 A 0.2390 0.4406 0.3204 54 L 0.2185 0.4224 0.3591 55 T 0.1385 0.4148 0.4467 56 D 0.1067 0.3025 0.5909 57 K 0.1407 0.2770 0.5823 58 A 0.2333 0.3018 0.4649 59 I 0.4042 0.2744 0.3214 60 V 0.5449 0.2197 0.2354 61 K 0.5526 0.2162 0.2312 62 K 0.4668 0.2805 0.2527 63 E 0.3853 0.2810 0.3337 64 L 0.3476 0.2988 0.3536 65 L 0.3489 0.3569 0.2941 66 Y 0.3627 0.3894 0.2479 67 D 0.3032 0.3979 0.2989 68 V 0.2517 0.4073 0.3410 69 A 0.2256 0.3038 0.4706 70 G 0.1409 0.1889 0.6702 71 S 0.1006 0.1183 0.7811 72 D 0.1861 0.1280 0.6859 73 K 0.2891 0.1384 0.5724 74 Y 0.4326 0.1368 0.4305 75 Q 0.5107 0.1022 0.3871 76 V 0.4880 0.0885 0.4234 77 N 0.3373 0.0734 0.5892 78 N 0.2820 0.0797 0.6383 79 K 0.3736 0.0988 0.5277 80 H 0.4188 0.1061 0.4751 81 D 0.3292 0.1169 0.5539 82 D 0.2444 0.1466 0.6090 83 K 0.1877 0.1182 0.6940 84 Y 0.1284 0.0848 0.7869 85 S 0.0743 0.0472 0.8785 86 P 0.0424 0.0415 0.9161 87 L 0.0305 0.0564 0.9131 88 P 0.0215 0.0797 0.8988 89 C 0.0117 0.5207 0.4676 90 S 0.0073 0.7920 0.2007 91 K 0.0064 0.9183 0.0754 92 I 0.0063 0.9510 0.0426 93 I 0.0062 0.9610 0.0329 94 Q 0.0050 0.9674 0.0276 95 R 0.0041 0.9697 0.0262 96 A 0.0040 0.9677 0.0282 97 E 0.0041 0.9594 0.0365 98 E 0.0045 0.9285 0.0670 99 L 0.0052 0.8429 0.1518 100 V 0.0093 0.6631 0.3276 101 G 0.0127 0.2872 0.7001 102 Q 0.0281 0.1077 0.8642 103 E 0.1056 0.0769 0.8175 104 V 0.1912 0.0790 0.7298 105 L 0.2309 0.1034 0.6656 106 Y 0.3562 0.1902 0.4536 107 K 0.3699 0.2477 0.3824 108 L 0.3816 0.3241 0.2943 109 T 0.3694 0.3575 0.2730 110 S 0.2775 0.3998 0.3227 111 E 0.1258 0.3948 0.4794 112 N 0.0868 0.3750 0.5382 113 C 0.0536 0.6081 0.3383 114 E 0.0314 0.7958 0.1727 115 H 0.0455 0.7973 0.1571 116 F 0.0215 0.9146 0.0639 117 V 0.0197 0.9365 0.0437 118 N 0.0209 0.9308 0.0483 119 E 0.0232 0.9303 0.0466 120 L 0.0381 0.9030 0.0588 121 R 0.0409 0.8404 0.1187 122 Y 0.0155 0.4989 0.4856 123 G 0.0245 0.0909 0.8846 124 V 0.0714 0.0478 0.8807 125 A 0.1476 0.0773 0.7751 126 R 0.1490 0.1865 0.6645 127 S 0.1411 0.2255 0.6334 128 D 0.1447 0.2923 0.5630 129 Q 0.2107 0.2027 0.5866 130 V 0.2384 0.1242 0.6373 131 R 0.1449 0.0704 0.7847 132 D 0.0105 0.0051 0.9844