# This file is the result of combining several RDB files, specifically # T0352.t04.dssp-ebghstl.rdb (weight 1.53986) # T0352.t04.stride-ebghtl.rdb (weight 1.24869) # T0352.t04.str2.rdb (weight 1.54758) # T0352.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 T0352.t04.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.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 15.1991 # # ============================================ # Comments from T0352.t04.stride-ebghtl.rdb # ============================================ # TARGET T0352 # 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 T0352.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 15.1991 # # ============================================ # Comments from T0352.t04.str2.rdb # ============================================ # TARGET T0352 # 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 T0352.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 15.1991 # # ============================================ # Comments from T0352.t04.alpha.rdb # ============================================ # TARGET T0352 # 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 T0352.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 15.1991 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0681 0.0243 0.9077 2 T 0.0657 0.0692 0.8651 3 T 0.0315 0.4794 0.4891 4 H 0.0153 0.8018 0.1829 5 D 0.0067 0.9217 0.0715 6 R 0.0056 0.9440 0.0504 7 V 0.0047 0.9557 0.0396 8 R 0.0047 0.9603 0.0351 9 L 0.0047 0.9566 0.0387 10 Q 0.0047 0.9534 0.0419 11 L 0.0047 0.9600 0.0353 12 Q 0.0046 0.9615 0.0339 13 A 0.0046 0.9611 0.0343 14 L 0.0047 0.9598 0.0355 15 E 0.0047 0.9606 0.0347 16 A 0.0046 0.9594 0.0359 17 L 0.0047 0.9564 0.0389 18 L 0.0047 0.9480 0.0473 19 R 0.0049 0.9156 0.0796 20 E 0.0060 0.8564 0.1376 21 H 0.0362 0.6333 0.3305 22 Q 0.0235 0.3600 0.6165 23 H 0.0559 0.3237 0.6204 24 W 0.1226 0.3073 0.5701 25 R 0.1198 0.2416 0.6386 26 N 0.0957 0.1384 0.7659 27 D 0.0746 0.0476 0.8777 28 E 0.0741 0.0194 0.9066 29 P 0.0801 0.0173 0.9026 30 Q 0.0736 0.0275 0.8989 31 P 0.0102 0.7688 0.2209 32 H 0.0114 0.7958 0.1927 33 Q 0.0157 0.8096 0.1747 34 F 0.0765 0.5420 0.3815 35 N 0.0562 0.2937 0.6501 36 S 0.0752 0.1189 0.8058 37 T 0.0644 0.1065 0.8291 38 Q 0.0906 0.0375 0.8720 39 P 0.1570 0.0725 0.7705 40 F 0.4379 0.0998 0.4623 41 F 0.5271 0.1140 0.3589 42 M 0.4743 0.1368 0.3889 43 D 0.3706 0.1161 0.5133 44 T 0.1887 0.1190 0.6923 45 M 0.1150 0.0822 0.8028 46 E 0.0817 0.1303 0.7880 47 P 0.0132 0.8162 0.1706 48 L 0.0169 0.8391 0.1440 49 E 0.0145 0.8912 0.0943 50 W 0.0229 0.8989 0.0782 51 L 0.0276 0.8888 0.0836 52 Q 0.0136 0.9315 0.0549 53 W 0.0142 0.9364 0.0494 54 V 0.0245 0.9007 0.0748 55 L 0.0235 0.8874 0.0891 56 I 0.0284 0.8497 0.1219 57 P 0.0153 0.8442 0.1405 58 R 0.0161 0.8255 0.1584 59 M 0.0049 0.9445 0.0507 60 H 0.0048 0.9531 0.0421 61 D 0.0047 0.9570 0.0383 62 L 0.0050 0.9526 0.0424 63 L 0.0053 0.9369 0.0578 64 D 0.0064 0.8507 0.1429 65 N 0.0423 0.5066 0.4511 66 K 0.0308 0.1731 0.7961 67 Q 0.0593 0.0216 0.9191 68 P 0.1042 0.0296 0.8662 69 L 0.0896 0.0230 0.8874 70 P 0.0586 0.0922 0.8492 71 G 0.0289 0.1821 0.7890 72 A 0.0851 0.2946 0.6203 73 F 0.1892 0.2544 0.5564 74 A 0.3060 0.2240 0.4700 75 V 0.2343 0.3262 0.4395 76 A 0.0869 0.6053 0.3079 77 P 0.0287 0.8611 0.1102 78 Y 0.0239 0.9004 0.0758 79 Y 0.0144 0.9365 0.0492 80 E 0.0137 0.9388 0.0475 81 M 0.0081 0.9440 0.0480 82 A 0.0086 0.9244 0.0670 83 L 0.0136 0.8639 0.1225 84 A 0.0164 0.7327 0.2508 85 T 0.0300 0.4929 0.4770 86 D 0.0392 0.2780 0.6828 87 H 0.0468 0.2149 0.7383 88 P 0.0194 0.5169 0.4637 89 Q 0.0161 0.7378 0.2460 90 R 0.0101 0.8851 0.1048 91 A 0.0075 0.9353 0.0572 92 L 0.0071 0.9434 0.0495 93 I 0.0054 0.9496 0.0451 94 L 0.0047 0.9586 0.0368 95 A 0.0047 0.9583 0.0371 96 E 0.0047 0.9553 0.0399 97 L 0.0047 0.9558 0.0395 98 E 0.0050 0.9545 0.0405 99 K 0.0049 0.9489 0.0462 100 L 0.0049 0.9498 0.0453 101 D 0.0050 0.9488 0.0463 102 A 0.0050 0.9416 0.0534 103 L 0.0063 0.9085 0.0852 104 F 0.0140 0.7772 0.2087 105 A 0.0233 0.5510 0.4257 106 D 0.0325 0.3156 0.6519 107 D 0.0384 0.1953 0.7662 108 A 0.0341 0.1528 0.8131 109 S 0.0380 0.0668 0.8952