# This file is the result of combining several RDB files, specifically # T0363.t04.dssp-ebghstl.rdb (weight 1.53986) # T0363.t04.stride-ebghtl.rdb (weight 1.24869) # T0363.t04.str2.rdb (weight 1.54758) # T0363.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 T0363.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0363 # Using neural net t06-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 T0363.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 16.3435 # # ============================================ # Comments from T0363.t04.stride-ebghtl.rdb # ============================================ # TARGET T0363 # 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 T0363.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 16.3435 # # ============================================ # Comments from T0363.t04.str2.rdb # ============================================ # TARGET T0363 # 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 T0363.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 16.3435 # # ============================================ # Comments from T0363.t04.alpha.rdb # ============================================ # TARGET T0363 # 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 T0363.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 16.3435 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1096 0.1518 0.7386 2 A 0.1504 0.2101 0.6395 3 H 0.1527 0.2145 0.6328 4 H 0.1394 0.1949 0.6657 5 H 0.1557 0.1844 0.6600 6 H 0.2063 0.1525 0.6412 7 H 0.2316 0.1506 0.6178 8 H 0.2342 0.1278 0.6380 9 S 0.2470 0.1142 0.6388 10 L 0.2175 0.1929 0.5897 11 N 0.2216 0.1587 0.6197 12 Q 0.6180 0.0566 0.3254 13 I 0.8346 0.0055 0.1599 14 N 0.9075 0.0037 0.0889 15 I 0.9219 0.0036 0.0745 16 E 0.9175 0.0043 0.0782 17 I 0.9287 0.0031 0.0682 18 A 0.9124 0.0048 0.0827 19 Y 0.8894 0.0045 0.1061 20 A 0.6702 0.0116 0.3183 21 F 0.3175 0.0148 0.6678 22 P 0.1198 0.1127 0.7675 23 E 0.0716 0.1838 0.7445 24 R 0.1905 0.2139 0.5956 25 Y 0.5529 0.0541 0.3931 26 Y 0.7923 0.0181 0.1896 27 L 0.8784 0.0075 0.1141 28 K 0.8501 0.0151 0.1348 29 S 0.8853 0.0074 0.1074 30 F 0.8648 0.0058 0.1293 31 Q 0.8541 0.0043 0.1416 32 V 0.5187 0.0143 0.4670 33 D 0.1277 0.0246 0.8476 34 E 0.0202 0.0842 0.8956 35 G 0.0270 0.0387 0.9343 36 I 0.1751 0.0201 0.8048 37 T 0.2248 0.0401 0.7350 38 V 0.0088 0.9466 0.0446 39 Q 0.0054 0.9596 0.0350 40 T 0.0052 0.9596 0.0353 41 A 0.0049 0.9603 0.0348 42 I 0.0047 0.9584 0.0369 43 T 0.0050 0.9408 0.0542 44 Q 0.0055 0.8838 0.1106 45 S 0.0406 0.5670 0.3924 46 G 0.0184 0.3007 0.6809 47 I 0.0393 0.5060 0.4547 48 L 0.0380 0.6430 0.3191 49 S 0.0388 0.5665 0.3947 50 Q 0.0497 0.3941 0.5561 51 F 0.0814 0.0572 0.8614 52 P 0.0303 0.1992 0.7705 53 E 0.0795 0.2440 0.6765 54 I 0.2182 0.1427 0.6391 55 D 0.1866 0.0633 0.7502 56 L 0.0449 0.4227 0.5324 57 S 0.0372 0.3319 0.6309 58 T 0.0600 0.3120 0.6280 59 N 0.2061 0.0623 0.7316 60 K 0.4676 0.0425 0.4899 61 I 0.8102 0.0163 0.1735 62 G 0.8361 0.0137 0.1502 63 I 0.8565 0.0139 0.1296 64 F 0.7237 0.0213 0.2550 65 S 0.5001 0.0278 0.4721 66 R 0.4865 0.0142 0.4993 67 P 0.5949 0.0162 0.3890 68 I 0.5082 0.0212 0.4706 69 K 0.3546 0.0225 0.6229 70 L 0.0895 0.3570 0.5536 71 T 0.0601 0.4230 0.5168 72 D 0.1232 0.3171 0.5597 73 V 0.2769 0.2451 0.4780 74 L 0.2645 0.1611 0.5744 75 K 0.1477 0.1179 0.7344 76 E 0.0410 0.1740 0.7850 77 G 0.0324 0.0608 0.9068 78 D 0.1361 0.0256 0.8383 79 R 0.6880 0.0088 0.3032 80 I 0.8718 0.0091 0.1191 81 E 0.8960 0.0153 0.0886 82 I 0.8873 0.0143 0.0984 83 Y 0.7788 0.0273 0.1938 84 R 0.5687 0.0513 0.3801 85 P 0.3525 0.1041 0.5434 86 L 0.3139 0.1394 0.5466 87 L 0.3380 0.0831 0.5789 88 A 0.2382 0.0345 0.7273 89 D 0.1438 0.0228 0.8334 90 P 0.0084 0.8310 0.1606 91 K 0.0066 0.8959 0.0974 92 E 0.0086 0.9181 0.0732 93 I 0.0164 0.8830 0.1006 94 R 0.0421 0.7720 0.1859 95 R 0.0483 0.5982 0.3536 96 E 0.0481 0.1824 0.7695 97 G 0.0350 0.0298 0.9352