# This file is the result of combining several RDB files, specifically # T0335.t06.dssp-ebghstl.rdb (weight 1.53986) # T0335.t06.stride-ebghtl.rdb (weight 1.24869) # T0335.t06.str2.rdb (weight 1.54758) # T0335.t06.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 T0335.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0335 # 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 T0335.t06-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 10.373 # # ============================================ # Comments from T0335.t06.stride-ebghtl.rdb # ============================================ # TARGET T0335 # Using neural net t06-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 T0335.t06-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 10.373 # # ============================================ # Comments from T0335.t06.str2.rdb # ============================================ # TARGET T0335 # Using neural net t06-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 T0335.t06-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 10.373 # # ============================================ # Comments from T0335.t06.alpha.rdb # ============================================ # TARGET T0335 # Using neural net t06-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 T0335.t06-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 10.373 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0294 0.1575 0.8131 2 I 0.0530 0.2800 0.6670 3 S 0.0380 0.4742 0.4878 4 N 0.0136 0.8076 0.1789 5 A 0.0104 0.8867 0.1030 6 K 0.0066 0.9314 0.0621 7 I 0.0054 0.9442 0.0505 8 A 0.0048 0.9511 0.0441 9 R 0.0047 0.9528 0.0425 10 I 0.0047 0.9553 0.0400 11 N 0.0047 0.9543 0.0410 12 E 0.0047 0.9517 0.0436 13 L 0.0048 0.9361 0.0590 14 A 0.0049 0.9119 0.0832 15 A 0.0056 0.8677 0.1266 16 K 0.0095 0.8143 0.1763 17 A 0.0170 0.7546 0.2284 18 K 0.0188 0.7123 0.2689 19 A 0.0341 0.5463 0.4196 20 G 0.0343 0.2438 0.7219 21 V 0.0492 0.1127 0.8381 22 I 0.1091 0.0297 0.8613 23 T 0.0551 0.0221 0.9228 24 E 0.0048 0.9451 0.0501 25 E 0.0047 0.9503 0.0450 26 E 0.0049 0.9529 0.0422 27 K 0.0047 0.9586 0.0367 28 A 0.0046 0.9591 0.0363 29 E 0.0047 0.9555 0.0398 30 Q 0.0047 0.9572 0.0381 31 Q 0.0046 0.9577 0.0376 32 K 0.0047 0.9522 0.0432 33 L 0.0047 0.9489 0.0464 34 R 0.0047 0.9575 0.0378 35 Q 0.0047 0.9599 0.0354 36 E 0.0049 0.9559 0.0392 37 Y 0.0048 0.9536 0.0416 38 L 0.0047 0.9560 0.0393 39 K 0.0049 0.9544 0.0407 40 G 0.0050 0.9445 0.0505 41 F 0.0053 0.9395 0.0552 42 R 0.0053 0.9445 0.0502 43 S 0.0051 0.9411 0.0538 44 S 0.0051 0.9296 0.0654 45 M 0.0053 0.9290 0.0657 46 K 0.0065 0.9151 0.0784 47 N 0.0098 0.8704 0.1197 48 T 0.0156 0.7722 0.2122 49 L 0.0806 0.6117 0.3077 50 K 0.1192 0.3640 0.5168 51 S 0.1978 0.2551 0.5470 52 V 0.5589 0.0595 0.3816 53 K 0.8042 0.0241 0.1717 54 I 0.8746 0.0094 0.1160 55 I 0.7762 0.0113 0.2126 56 D 0.1713 0.0129 0.8158 57 P 0.0085 0.1329 0.8585 58 E 0.0426 0.0383 0.9191 59 G 0.0562 0.0492 0.8946 60 N 0.0872 0.0642 0.8486 61 D 0.3706 0.0418 0.5877 62 V 0.2572 0.0258 0.7170 63 T 0.0982 0.0179 0.8839 64 P 0.0073 0.9117 0.0810 65 E 0.0049 0.9469 0.0482 66 K 0.0050 0.9493 0.0457 67 L 0.0068 0.9430 0.0502 68 K 0.0065 0.9367 0.0569 69 R 0.0064 0.9273 0.0664 70 E 0.0074 0.9011 0.0916 71 Q 0.0123 0.8547 0.1330 72 R 0.0155 0.7904 0.1941 73 N 0.0213 0.6309 0.3479 74 N 0.0400 0.3790 0.5811 75 K 0.0483 0.2477 0.7040 76 L 0.0663 0.1274 0.8063 77 H 0.0484 0.0327 0.9189