# This file is the result of combining several RDB files, specifically # T0221.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0221.t2k.stride-ebghtl.rdb (weight 1.24869) # T0221.t2k.str2.rdb (weight 1.54758) # T0221.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 T0221.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0221 # 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 T0221.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 658 # # ============================================ # Comments from T0221.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0221 # 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 T0221.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 658 # # ============================================ # Comments from T0221.t2k.str2.rdb # ============================================ # TARGET T0221 # 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 T0221.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 658 # # ============================================ # Comments from T0221.t2k.alpha.rdb # ============================================ # TARGET T0221 # 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 T0221.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 658 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0740 0.1164 0.8096 2 K 0.0949 0.0803 0.8248 3 T 0.0925 0.0411 0.8664 4 I 0.0815 0.0941 0.8244 5 Q 0.0548 0.3216 0.6236 6 P 0.0363 0.3967 0.5670 7 C 0.0469 0.3042 0.6490 8 S 0.0425 0.3976 0.5598 9 V 0.0180 0.6892 0.2928 10 E 0.0081 0.8622 0.1297 11 D 0.0069 0.9207 0.0725 12 I 0.0049 0.9471 0.0480 13 Q 0.0047 0.9549 0.0404 14 S 0.0048 0.9525 0.0427 15 W 0.0047 0.9570 0.0382 16 L 0.0047 0.9586 0.0367 17 I 0.0047 0.9606 0.0347 18 D 0.0047 0.9607 0.0346 19 Q 0.0047 0.9601 0.0352 20 F 0.0047 0.9589 0.0364 21 A 0.0048 0.9577 0.0376 22 Q 0.0056 0.9449 0.0495 23 Q 0.0070 0.9158 0.0772 24 L 0.0467 0.6482 0.3050 25 D 0.0413 0.0751 0.8836 26 V 0.0563 0.0139 0.9298 27 D 0.0714 0.0196 0.9089 28 P 0.0104 0.8121 0.1775 29 D 0.0097 0.7843 0.2060 30 D 0.0324 0.7288 0.2387 31 I 0.1683 0.1152 0.7165 32 D 0.1333 0.0542 0.8125 33 M 0.0272 0.4407 0.5321 34 E 0.0214 0.4622 0.5164 35 E 0.0542 0.4884 0.4574 36 S 0.0615 0.5579 0.3805 37 F 0.0379 0.7574 0.2047 38 D 0.0219 0.8151 0.1629 39 N 0.0207 0.7608 0.2185 40 Y 0.0463 0.5079 0.4458 41 D 0.0454 0.1197 0.8349 42 L 0.0683 0.1477 0.7840 43 N 0.0652 0.2437 0.6911 44 S 0.0885 0.6715 0.2400 45 S 0.0555 0.8565 0.0881 46 K 0.0233 0.9161 0.0606 47 A 0.0159 0.9381 0.0460 48 L 0.0085 0.9513 0.0402 49 I 0.0079 0.9532 0.0389 50 L 0.0047 0.9567 0.0386 51 L 0.0047 0.9587 0.0366 52 G 0.0048 0.9578 0.0375 53 R 0.0048 0.9582 0.0370 54 L 0.0047 0.9585 0.0368 55 E 0.0048 0.9538 0.0414 56 K 0.0055 0.9376 0.0568 57 W 0.0075 0.9001 0.0923 58 L 0.0455 0.5092 0.4453 59 G 0.0293 0.0423 0.9284 60 K 0.0810 0.0236 0.8954 61 E 0.1675 0.0221 0.8104 62 L 0.2107 0.0439 0.7455 63 N 0.1527 0.0695 0.7777 64 P 0.0987 0.6095 0.2918 65 V 0.0959 0.6926 0.2115 66 L 0.1360 0.7246 0.1394 67 I 0.1455 0.6414 0.2131 68 F 0.1823 0.4307 0.3870 69 N 0.1243 0.2781 0.5977 70 Y 0.1018 0.0890 0.8093 71 P 0.1158 0.0394 0.8448 72 T 0.0970 0.0519 0.8511 73 I 0.0054 0.9256 0.0690 74 A 0.0048 0.9483 0.0469 75 Q 0.0050 0.9509 0.0441 76 L 0.0048 0.9516 0.0436 77 A 0.0048 0.9490 0.0462 78 K 0.0048 0.9348 0.0603 79 R 0.0049 0.9314 0.0637 80 L 0.0081 0.9030 0.0889 81 G 0.0059 0.8584 0.1357 82 E 0.0072 0.8023 0.1905 83 L 0.0107 0.6335 0.3558 84 Y 0.0285 0.4497 0.5218 85 L 0.0204 0.1614 0.8183