# This file is the result of combining several RDB files, specifically # T0335.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0335.t2k.stride-ebghtl.rdb (weight 1.24869) # T0335.t2k.str2.rdb (weight 1.54758) # T0335.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 T0335.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0335 # 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 T0335.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 54 # # ============================================ # Comments from T0335.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0335 # 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 T0335.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 54 # # ============================================ # Comments from T0335.t2k.str2.rdb # ============================================ # TARGET T0335 # 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 T0335.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 54 # # ============================================ # Comments from T0335.t2k.alpha.rdb # ============================================ # TARGET T0335 # 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 T0335.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 54 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0477 0.0800 0.8724 2 I 0.0781 0.1119 0.8100 3 S 0.0432 0.2865 0.6704 4 N 0.0053 0.9259 0.0688 5 A 0.0054 0.9371 0.0576 6 K 0.0048 0.9524 0.0428 7 I 0.0047 0.9580 0.0373 8 A 0.0047 0.9573 0.0380 9 R 0.0047 0.9563 0.0390 10 I 0.0047 0.9585 0.0368 11 N 0.0047 0.9557 0.0396 12 E 0.0048 0.9535 0.0418 13 L 0.0049 0.9504 0.0447 14 A 0.0086 0.9316 0.0598 15 A 0.0078 0.9097 0.0825 16 K 0.0104 0.9076 0.0820 17 A 0.0089 0.8942 0.0969 18 K 0.0110 0.8039 0.1852 19 A 0.0221 0.6585 0.3194 20 G 0.0419 0.2976 0.6604 21 V 0.0369 0.1061 0.8570 22 I 0.0538 0.0320 0.9142 23 T 0.0470 0.0279 0.9251 24 E 0.0051 0.9065 0.0884 25 E 0.0048 0.9263 0.0689 26 E 0.0048 0.9356 0.0596 27 K 0.0047 0.9488 0.0465 28 A 0.0048 0.9430 0.0523 29 E 0.0048 0.9424 0.0528 30 Q 0.0049 0.9477 0.0474 31 Q 0.0049 0.9521 0.0430 32 K 0.0048 0.9534 0.0418 33 L 0.0048 0.9509 0.0443 34 R 0.0048 0.9564 0.0389 35 Q 0.0049 0.9558 0.0393 36 E 0.0049 0.9541 0.0410 37 Y 0.0048 0.9520 0.0432 38 L 0.0047 0.9537 0.0416 39 K 0.0049 0.9485 0.0466 40 G 0.0048 0.9359 0.0593 41 F 0.0047 0.9373 0.0580 42 R 0.0047 0.9483 0.0469 43 S 0.0049 0.9424 0.0527 44 S 0.0050 0.9266 0.0684 45 M 0.0054 0.9356 0.0590 46 K 0.0058 0.9290 0.0652 47 N 0.0093 0.8743 0.1164 48 T 0.0150 0.7915 0.1935 49 L 0.0964 0.5273 0.3763 50 K 0.0634 0.2781 0.6586 51 S 0.1439 0.1033 0.7528 52 V 0.4632 0.0180 0.5187 53 K 0.7455 0.0057 0.2488 54 I 0.8435 0.0051 0.1515 55 I 0.8249 0.0079 0.1672 56 D 0.3302 0.0141 0.6557 57 P 0.0130 0.1228 0.8642 58 E 0.0463 0.0272 0.9265 59 G 0.0406 0.0467 0.9128 60 N 0.1201 0.0361 0.8437 61 D 0.4056 0.0236 0.5709 62 V 0.2797 0.0242 0.6960 63 T 0.0894 0.0407 0.8699 64 P 0.0129 0.8681 0.1191 65 E 0.0070 0.9364 0.0566 66 K 0.0055 0.9479 0.0467 67 L 0.0047 0.9540 0.0413 68 K 0.0048 0.9525 0.0426 69 R 0.0047 0.9515 0.0438 70 E 0.0047 0.9483 0.0470 71 Q 0.0048 0.9401 0.0551 72 R 0.0050 0.9191 0.0759 73 N 0.0067 0.8630 0.1304 74 N 0.0402 0.5169 0.4430 75 K 0.0320 0.2052 0.7628 76 L 0.0385 0.1069 0.8546 77 H 0.0454 0.0433 0.9113