# This file is the result of combining several RDB files, specifically # T0262.t04.dssp-ebghstl.rdb (weight 1.53986) # T0262.t04.stride-ebghtl.rdb (weight 1.24869) # T0262.t04.str2.rdb (weight 1.54758) # T0262.t04.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 T0262.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0262 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0262.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 13.6155 # # ============================================ # Comments from T0262.t04.stride-ebghtl.rdb # ============================================ # TARGET T0262 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0262.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 13.6155 # # ============================================ # Comments from T0262.t04.str2.rdb # ============================================ # TARGET T0262 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0262.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 13.6155 # # ============================================ # Comments from T0262.t04.alpha.rdb # ============================================ # TARGET T0262 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0262.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 13.6155 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.0490 0.2048 0.7461 2 S 0.0439 0.3724 0.5837 3 K 0.0096 0.8880 0.1024 4 T 0.0181 0.9058 0.0760 5 L 0.0279 0.9139 0.0582 6 A 0.0388 0.9053 0.0559 7 G 0.0506 0.8962 0.0531 8 I 0.0413 0.8892 0.0694 9 L 0.0515 0.8187 0.1298 10 R 0.0704 0.5344 0.3952 11 H 0.0827 0.2764 0.6409 12 H 0.0837 0.0479 0.8684 13 P 0.0360 0.2224 0.7416 14 G 0.0529 0.2633 0.6838 15 R 0.2161 0.2911 0.4928 16 Y 0.3042 0.0915 0.6043 17 G 0.4048 0.0400 0.5552 18 V 0.6515 0.0089 0.3396 19 R 0.7969 0.0045 0.1986 20 L 0.7033 0.0092 0.2875 21 T 0.2697 0.0260 0.7043 22 R 0.0417 0.1355 0.8229 23 E 0.0502 0.0639 0.8859 24 G 0.2028 0.0553 0.7419 25 W 0.5612 0.0162 0.4226 26 A 0.7633 0.0089 0.2277 27 R 0.6146 0.0161 0.3693 28 V 0.0118 0.9280 0.0602 29 S 0.0066 0.9515 0.0419 30 E 0.0056 0.9536 0.0408 31 V 0.0067 0.9515 0.0418 32 V 0.0052 0.9548 0.0400 33 E 0.0049 0.9523 0.0428 34 G 0.0049 0.9476 0.0475 35 L 0.0053 0.9379 0.0569 36 R 0.0063 0.9161 0.0776 37 K 0.0070 0.8686 0.1244 38 A 0.0434 0.4438 0.5128 39 G 0.0319 0.0535 0.9145 40 W 0.0769 0.0399 0.8832 41 S 0.0872 0.1184 0.7944 42 W 0.2270 0.1357 0.6373 43 V 0.2760 0.0621 0.6619 44 E 0.2193 0.0734 0.7073 45 E 0.0247 0.8812 0.0941 46 W 0.0297 0.8578 0.1124 47 H 0.0681 0.8097 0.1221 48 I 0.1844 0.7141 0.1015 49 V 0.2112 0.6908 0.0981 50 G 0.2832 0.6319 0.0849 51 V 0.2940 0.6232 0.0828 52 A 0.3265 0.5596 0.1139 53 L 0.3246 0.4448 0.2306 54 H 0.2454 0.2348 0.5198 55 D 0.0957 0.0209 0.8835 56 P 0.0158 0.1486 0.8356 57 K 0.0629 0.0796 0.8574 58 G 0.0997 0.1070 0.7933 59 R 0.3880 0.0619 0.5501 60 Y 0.8076 0.0220 0.1704 61 E 0.8640 0.0141 0.1219 62 L 0.8021 0.0164 0.1815 63 R 0.5991 0.0274 0.3735 64 N 0.1340 0.0435 0.8225 65 G 0.1507 0.0367 0.8126 66 E 0.7277 0.0136 0.2587 67 I 0.8728 0.0039 0.1233 68 R 0.8596 0.0078 0.1326 69 A 0.8087 0.0181 0.1733 70 R 0.7306 0.0384 0.2310 71 Y 0.6551 0.0378 0.3071 72 G 0.4431 0.0374 0.5194 73 H 0.4459 0.0329 0.5213 74 S 0.4326 0.0281 0.5394 75 I 0.4544 0.0168 0.5289 76 P 0.4438 0.0114 0.5448 77 V 0.4520 0.0135 0.5345 78 N 0.5204 0.0107 0.4688 79 V 0.3623 0.0241 0.6136 80 E 0.2646 0.0180 0.7175 81 P 0.2131 0.0284 0.7585 82 L 0.0994 0.0182 0.8824 83 P 0.0801 0.0449 0.8750 84 G 0.0640 0.0389 0.8970 85 E 0.0834 0.0164 0.9001 86 P 0.0784 0.0126 0.9090 87 P 0.1005 0.0241 0.8754 88 P 0.1595 0.0770 0.7634 89 I 0.6550 0.0395 0.3054 90 L 0.8328 0.0159 0.1514 91 Y 0.8231 0.0150 0.1619 92 H 0.6796 0.0301 0.2903 93 G 0.2819 0.0405 0.6776 94 T 0.1538 0.0610 0.7852 95 T 0.0746 0.3640 0.5614 96 E 0.0133 0.8466 0.1401 97 E 0.0108 0.8677 0.1216 98 A 0.0104 0.8632 0.1263 99 L 0.0057 0.9365 0.0578 100 P 0.0048 0.9526 0.0427 101 L 0.0047 0.9578 0.0375 102 I 0.0047 0.9579 0.0374 103 M 0.0049 0.9515 0.0435 104 E 0.0061 0.9290 0.0648 105 R 0.0379 0.5441 0.4181 106 G 0.0283 0.0973 0.8745 107 I 0.0893 0.0582 0.8526 108 M 0.1324 0.0589 0.8087 109 R 0.0897 0.1649 0.7454 110 G 0.0676 0.1234 0.8090 111 R 0.1372 0.1193 0.7436 112 R 0.3856 0.0717 0.5427 113 L 0.4867 0.0653 0.4479 114 K 0.8124 0.0204 0.1672 115 V 0.8574 0.0130 0.1297 116 H 0.8339 0.0154 0.1507 117 L 0.6218 0.0271 0.3511 118 T 0.2857 0.0414 0.6729 119 S 0.1368 0.1161 0.7471 120 S 0.1119 0.1108 0.7773 121 L 0.0705 0.5237 0.4058 122 E 0.0515 0.5984 0.3502 123 D 0.0505 0.4897 0.4598 124 A 0.0653 0.3539 0.5808 125 V 0.0696 0.1202 0.8102 126 S 0.0455 0.0404 0.9141