# This file is the result of combining several RDB files, specifically # T0330.t04.dssp-ebghstl.rdb (weight 1.53986) # T0330.t04.stride-ebghtl.rdb (weight 1.24869) # T0330.t04.str2.rdb (weight 1.54758) # T0330.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 T0330.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 3.54411 # # ============================================ # Comments from T0330.t04.stride-ebghtl.rdb # ============================================ # TARGET T0330 # 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 T0330.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 3.54411 # # ============================================ # Comments from T0330.t04.str2.rdb # ============================================ # TARGET T0330 # 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 T0330.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 3.54411 # # ============================================ # Comments from T0330.t04.alpha.rdb # ============================================ # TARGET T0330 # 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 T0330.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 3.54411 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.1536 0.0149 0.8315 2 K 0.1914 0.0281 0.7805 3 V 0.1301 0.3263 0.5437 4 E 0.0691 0.5136 0.4173 5 S 0.0402 0.7609 0.1989 6 M 0.0250 0.8753 0.0997 7 N 0.0097 0.9164 0.0739 8 R 0.0050 0.9519 0.0431 9 R 0.0050 0.9581 0.0369 10 V 0.0050 0.9583 0.0367 11 L 0.0047 0.9557 0.0396 12 A 0.0047 0.9535 0.0418 13 D 0.0051 0.9423 0.0526 14 A 0.0062 0.9257 0.0682 15 L 0.0091 0.9286 0.0623 16 I 0.0168 0.9136 0.0696 17 E 0.0253 0.8937 0.0810 18 V 0.0613 0.8041 0.1346 19 Y 0.1263 0.5207 0.3530 20 G 0.1091 0.1456 0.7453 21 T 0.1200 0.0771 0.8029 22 E 0.1146 0.1007 0.7847 23 G 0.1123 0.0768 0.8109 24 S 0.1294 0.0912 0.7795 25 T 0.1289 0.1543 0.7168 26 G 0.1485 0.1261 0.7254 27 S 0.2166 0.1374 0.6460 28 H 0.2718 0.1171 0.6111 29 D 0.2301 0.1080 0.6619 30 F 0.2195 0.1613 0.6192 31 S 0.2232 0.1723 0.6045 32 G 0.2337 0.1635 0.6028 33 K 0.1830 0.2733 0.5437 34 M 0.1817 0.2495 0.5688 35 D 0.0921 0.2876 0.6203 36 G 0.0522 0.5121 0.4357 37 A 0.1977 0.6345 0.1677 38 I 0.2633 0.6665 0.0702 39 I 0.1855 0.7612 0.0533 40 Y 0.1525 0.7948 0.0528 41 E 0.0699 0.8681 0.0620 42 V 0.0486 0.8798 0.0716 43 L 0.0421 0.8747 0.0832 44 S 0.0287 0.8358 0.1355 45 N 0.0157 0.7591 0.2251 46 V 0.0476 0.4112 0.5412 47 G 0.0420 0.0921 0.8660 48 L 0.0985 0.0846 0.8169 49 E 0.0983 0.1464 0.7554 50 R 0.0241 0.7370 0.2389 51 A 0.0101 0.8698 0.1201 52 E 0.0110 0.8933 0.0957 53 I 0.0094 0.9131 0.0775 54 A 0.0070 0.9086 0.0844 55 D 0.0059 0.8950 0.0990 56 K 0.0058 0.8854 0.1088 57 F 0.0077 0.8674 0.1249 58 D 0.0052 0.9247 0.0701 59 K 0.0051 0.9392 0.0557 60 A 0.0050 0.9457 0.0493 61 K 0.0049 0.9502 0.0449 62 E 0.0048 0.9540 0.0412 63 T 0.0048 0.9547 0.0405 64 Y 0.0047 0.9569 0.0384 65 I 0.0047 0.9604 0.0349 66 A 0.0047 0.9604 0.0349 67 L 0.0047 0.9594 0.0359 68 F 0.0048 0.9545 0.0407 69 R 0.0052 0.9434 0.0513 70 E 0.0085 0.9061 0.0854 71 R 0.0158 0.7667 0.2175 72 A 0.0649 0.4820 0.4532 73 R 0.0749 0.2230 0.7021 74 R 0.0213 0.6640 0.3147 75 E 0.0176 0.5639 0.4185 76 D 0.0506 0.4582 0.4912 77 I 0.2193 0.2410 0.5397 78 T 0.2467 0.1368 0.6164 79 L 0.1166 0.0533 0.8301