# This file is the result of combining several RDB files, specifically # T0352.t06.dssp-ebghstl.rdb (weight 1.53986) # T0352.t06.stride-ebghtl.rdb (weight 1.24869) # T0352.t06.str2.rdb (weight 1.54758) # T0352.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 T0352.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0352 # 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 T0352.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 15.3431 # # ============================================ # Comments from T0352.t06.stride-ebghtl.rdb # ============================================ # TARGET T0352 # 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 T0352.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 15.3431 # # ============================================ # Comments from T0352.t06.str2.rdb # ============================================ # TARGET T0352 # 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 T0352.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 15.3431 # # ============================================ # Comments from T0352.t06.alpha.rdb # ============================================ # TARGET T0352 # 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 T0352.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 15.3431 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0601 0.0291 0.9108 2 T 0.0700 0.0866 0.8433 3 T 0.0445 0.3704 0.5851 4 H 0.0199 0.6510 0.3291 5 D 0.0063 0.8985 0.0951 6 R 0.0062 0.9311 0.0627 7 V 0.0047 0.9517 0.0436 8 R 0.0047 0.9580 0.0373 9 L 0.0047 0.9554 0.0400 10 Q 0.0047 0.9528 0.0425 11 L 0.0047 0.9599 0.0355 12 Q 0.0046 0.9614 0.0340 13 A 0.0046 0.9604 0.0349 14 L 0.0047 0.9587 0.0366 15 E 0.0047 0.9605 0.0348 16 A 0.0047 0.9592 0.0361 17 L 0.0047 0.9554 0.0399 18 L 0.0047 0.9490 0.0463 19 R 0.0049 0.9143 0.0809 20 E 0.0064 0.8472 0.1464 21 H 0.0432 0.5998 0.3570 22 Q 0.0294 0.3055 0.6652 23 H 0.0523 0.3388 0.6089 24 W 0.1241 0.3347 0.5412 25 R 0.1268 0.2567 0.6165 26 N 0.1101 0.1522 0.7376 27 D 0.0824 0.0597 0.8579 28 E 0.0723 0.0274 0.9003 29 P 0.0802 0.0208 0.8991 30 Q 0.0766 0.0303 0.8931 31 P 0.0105 0.7668 0.2227 32 H 0.0089 0.8013 0.1898 33 Q 0.0137 0.8042 0.1821 34 F 0.0794 0.5175 0.4031 35 N 0.0565 0.2541 0.6895 36 S 0.0929 0.1225 0.7846 37 T 0.0607 0.1068 0.8325 38 Q 0.0767 0.0392 0.8841 39 P 0.1207 0.0856 0.7937 40 F 0.3311 0.1245 0.5444 41 F 0.4614 0.1512 0.3873 42 M 0.4450 0.1754 0.3796 43 D 0.3328 0.1648 0.5024 44 T 0.1773 0.1319 0.6907 45 M 0.1258 0.1119 0.7623 46 E 0.0812 0.1652 0.7536 47 P 0.0094 0.8349 0.1557 48 L 0.0095 0.8680 0.1224 49 E 0.0123 0.9036 0.0841 50 W 0.0163 0.9202 0.0635 51 L 0.0127 0.9227 0.0647 52 Q 0.0169 0.9276 0.0555 53 W 0.0148 0.9331 0.0520 54 V 0.0240 0.8877 0.0883 55 L 0.0208 0.8617 0.1175 56 I 0.0280 0.8330 0.1389 57 P 0.0157 0.8272 0.1571 58 R 0.0166 0.8203 0.1631 59 M 0.0049 0.9389 0.0563 60 H 0.0048 0.9482 0.0469 61 D 0.0049 0.9511 0.0440 62 L 0.0053 0.9454 0.0493 63 L 0.0063 0.9242 0.0696 64 D 0.0094 0.8105 0.1801 65 N 0.0454 0.4164 0.5382 66 K 0.0306 0.1342 0.8351 67 Q 0.0568 0.0219 0.9214 68 P 0.1016 0.0326 0.8658 69 L 0.0844 0.0278 0.8878 70 P 0.0506 0.1239 0.8255 71 G 0.0274 0.2153 0.7573 72 A 0.0703 0.3434 0.5863 73 F 0.1643 0.2826 0.5531 74 A 0.2859 0.2554 0.4587 75 V 0.2193 0.3819 0.3988 76 A 0.0740 0.6628 0.2632 77 P 0.0354 0.8250 0.1395 78 Y 0.0233 0.8993 0.0774 79 Y 0.0178 0.9272 0.0550 80 E 0.0152 0.9356 0.0492 81 M 0.0116 0.9355 0.0529 82 A 0.0095 0.9238 0.0667 83 L 0.0143 0.8683 0.1174 84 A 0.0181 0.7415 0.2404 85 T 0.0235 0.4865 0.4900 86 D 0.0339 0.2515 0.7146 87 H 0.0481 0.1993 0.7526 88 P 0.0196 0.4478 0.5326 89 Q 0.0185 0.6742 0.3073 90 R 0.0122 0.8525 0.1353 91 A 0.0080 0.9210 0.0710 92 L 0.0098 0.9336 0.0565 93 I 0.0077 0.9439 0.0483 94 L 0.0054 0.9525 0.0421 95 A 0.0050 0.9544 0.0406 96 E 0.0048 0.9541 0.0410 97 L 0.0047 0.9552 0.0401 98 E 0.0048 0.9558 0.0394 99 K 0.0049 0.9493 0.0458 100 L 0.0048 0.9484 0.0467 101 D 0.0051 0.9459 0.0490 102 A 0.0053 0.9335 0.0612 103 L 0.0069 0.8927 0.1004 104 F 0.0172 0.7385 0.2443 105 A 0.0288 0.5026 0.4686 106 D 0.0380 0.2978 0.6642 107 D 0.0409 0.1968 0.7623 108 A 0.0407 0.1455 0.8137 109 S 0.0421 0.0480 0.9099