# This file is the result of combining several RDB files, specifically # T0239.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0239.t2k.stride-ebghtl.rdb (weight 1.24869) # T0239.t2k.str2.rdb (weight 1.54758) # T0239.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 T0239.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0239 # 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 T0239.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 1 # # ============================================ # Comments from T0239.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0239 # 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 T0239.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 1 # # ============================================ # Comments from T0239.t2k.str2.rdb # ============================================ # TARGET T0239 # 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 T0239.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 1 # # ============================================ # Comments from T0239.t2k.alpha.rdb # ============================================ # TARGET T0239 # 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 T0239.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0635 0.0497 0.8868 2 K 0.1477 0.0797 0.7726 3 K 0.2850 0.1048 0.6102 4 H 0.5057 0.0817 0.4126 5 I 0.7332 0.0378 0.2290 6 I 0.7934 0.0343 0.1723 7 I 0.7162 0.0458 0.2380 8 K 0.5963 0.0641 0.3396 9 T 0.4300 0.0605 0.5095 10 I 0.2602 0.0411 0.6987 11 P 0.1522 0.0775 0.7704 12 K 0.1013 0.1957 0.7030 13 K 0.0742 0.3914 0.5345 14 E 0.0785 0.5051 0.4164 15 E 0.1260 0.5139 0.3601 16 I 0.1899 0.4593 0.3507 17 I 0.2081 0.3801 0.4119 18 S 0.1998 0.3679 0.4322 19 R 0.1061 0.5005 0.3934 20 D 0.1146 0.4379 0.4475 21 L 0.1515 0.4369 0.4116 22 C 0.1940 0.3465 0.4595 23 D 0.2408 0.2926 0.4666 24 C 0.4157 0.2356 0.3487 25 I 0.5621 0.1786 0.2593 26 Y 0.6695 0.1154 0.2151 27 Y 0.5995 0.1129 0.2876 28 Y 0.4498 0.0995 0.4507 29 D 0.2125 0.1049 0.6825 30 N 0.1360 0.1022 0.7617 31 S 0.3802 0.0755 0.5443 32 V 0.7251 0.0314 0.2435 33 I 0.7578 0.0255 0.2168 34 C 0.6370 0.0283 0.3347 35 K 0.5142 0.0295 0.4563 36 P 0.3957 0.0350 0.5693 37 I 0.2530 0.0474 0.6997 38 G 0.1513 0.0351 0.8136 39 P 0.1191 0.1231 0.7579 40 S 0.1936 0.1455 0.6609 41 K 0.4427 0.1288 0.4285 42 V 0.6031 0.0900 0.3069 43 Y 0.6724 0.0780 0.2496 44 V 0.6387 0.0955 0.2657 45 S 0.4574 0.1458 0.3969 46 T 0.2680 0.2243 0.5077 47 S 0.2119 0.2465 0.5417 48 L 0.0696 0.5967 0.3337 49 E 0.0338 0.6522 0.3140 50 N 0.0323 0.6334 0.3342 51 L 0.0179 0.8041 0.1779 52 E 0.0142 0.8550 0.1308 53 K 0.0135 0.8705 0.1160 54 C 0.0179 0.8697 0.1124 55 L 0.0258 0.8444 0.1298 56 Q 0.0262 0.8343 0.1395 57 L 0.0227 0.8517 0.1255 58 H 0.0270 0.8399 0.1331 59 Y 0.0275 0.8229 0.1496 60 F 0.0206 0.8537 0.1257 61 K 0.0182 0.8612 0.1205 62 K 0.0246 0.8293 0.1460 63 L 0.0307 0.8113 0.1581 64 V 0.0549 0.7584 0.1867 65 K 0.0479 0.7255 0.2267 66 N 0.0686 0.6008 0.3305 67 I 0.1286 0.5716 0.2999 68 E 0.1679 0.5895 0.2426 69 I 0.1503 0.6046 0.2451 70 F 0.1452 0.5751 0.2798 71 D 0.1186 0.5870 0.2944 72 E 0.0998 0.5865 0.3138 73 V 0.1169 0.4999 0.3832 74 H 0.1093 0.3401 0.5506 75 N 0.0828 0.1965 0.7207 76 S 0.0797 0.1267 0.7936 77 K 0.0815 0.0778 0.8407 78 P 0.0452 0.1751 0.7796 79 N 0.0623 0.1642 0.7735 80 C 0.1160 0.1494 0.7346 81 D 0.1777 0.1346 0.6877 82 K 0.4050 0.1183 0.4766 83 C 0.6583 0.0574 0.2843 84 L 0.8148 0.0337 0.1515 85 I 0.8779 0.0188 0.1032 86 V 0.8576 0.0232 0.1192 87 E 0.8255 0.0239 0.1506 88 I 0.6476 0.0519 0.3005 89 G 0.2875 0.0450 0.6675 90 G 0.3583 0.0517 0.5900 91 V 0.7878 0.0240 0.1882 92 Y 0.8566 0.0223 0.1211 93 F 0.8662 0.0221 0.1116 94 V 0.8104 0.0338 0.1558 95 R 0.7219 0.0450 0.2331 96 R 0.6274 0.0436 0.3289 97 V 0.2914 0.0441 0.6644 98 N 0.0545 0.0250 0.9205