# This file is the result of combining several RDB files, specifically # T0358.t04.dssp-ebghstl.rdb (weight 1.53986) # T0358.t04.stride-ebghtl.rdb (weight 1.24869) # T0358.t04.str2.rdb (weight 1.54758) # T0358.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 T0358.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0358 # 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 T0358.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 5.93915 # # ============================================ # Comments from T0358.t04.stride-ebghtl.rdb # ============================================ # TARGET T0358 # 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 T0358.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 5.93915 # # ============================================ # Comments from T0358.t04.str2.rdb # ============================================ # TARGET T0358 # 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 T0358.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 5.93915 # # ============================================ # Comments from T0358.t04.alpha.rdb # ============================================ # TARGET T0358 # 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 T0358.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 5.93915 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1034 0.0492 0.8475 2 T 0.1637 0.0711 0.7652 3 Q 0.2240 0.1780 0.5980 4 S 0.3599 0.1617 0.4784 5 V 0.5236 0.0945 0.3819 6 L 0.4938 0.0438 0.4624 7 L 0.1847 0.0184 0.7969 8 P 0.0985 0.0170 0.8845 9 P 0.0569 0.0802 0.8629 10 G 0.0581 0.0608 0.8811 11 P 0.0709 0.2147 0.7144 12 F 0.1070 0.2835 0.6095 13 T 0.1072 0.3814 0.5114 14 R 0.0171 0.8544 0.1285 15 R 0.0268 0.8564 0.1168 16 Q 0.0409 0.8532 0.1059 17 A 0.0598 0.8547 0.0854 18 Q 0.1041 0.8107 0.0853 19 A 0.1529 0.7622 0.0849 20 V 0.2030 0.6974 0.0997 21 T 0.2770 0.5818 0.1412 22 T 0.2961 0.4715 0.2324 23 T 0.3302 0.2474 0.4225 24 Y 0.4278 0.1402 0.4320 25 S 0.3828 0.1235 0.4937 26 N 0.3870 0.0647 0.5483 27 I 0.5505 0.0296 0.4199 28 T 0.7356 0.0229 0.2416 29 L 0.7381 0.0405 0.2213 30 E 0.5453 0.0657 0.3889 31 D 0.2593 0.0584 0.6823 32 D 0.1028 0.0780 0.8192 33 Q 0.0699 0.0968 0.8333 34 G 0.0848 0.1072 0.8081 35 S 0.1757 0.1035 0.7208 36 H 0.4608 0.0544 0.4848 37 F 0.7708 0.0177 0.2115 38 R 0.8769 0.0101 0.1130 39 L 0.9230 0.0047 0.0723 40 V 0.9234 0.0054 0.0712 41 V 0.9178 0.0050 0.0772 42 R 0.8731 0.0109 0.1160 43 D 0.4230 0.0197 0.5573 44 T 0.0633 0.1209 0.8157 45 E 0.0519 0.0330 0.9151 46 G 0.0722 0.0340 0.8938 47 R 0.3613 0.0226 0.6161 48 M 0.8749 0.0043 0.1207 49 V 0.8985 0.0083 0.0932 50 W 0.9111 0.0071 0.0818 51 R 0.8738 0.0137 0.1126 52 A 0.7644 0.0319 0.2037 53 W 0.4244 0.0834 0.4922 54 N 0.2186 0.0559 0.7255 55 F 0.1451 0.0720 0.7829 56 E 0.0878 0.0755 0.8367 57 P 0.0349 0.2417 0.7234 58 D 0.0388 0.2316 0.7296 59 A 0.0487 0.3780 0.5733 60 G 0.0285 0.4358 0.5358 61 E 0.0263 0.6142 0.3595 62 G 0.0358 0.7215 0.2427 63 L 0.0329 0.8186 0.1484 64 N 0.0307 0.8490 0.1203 65 R 0.0273 0.8940 0.0788 66 Y 0.0369 0.8892 0.0739 67 I 0.0653 0.8475 0.0872 68 R 0.0584 0.7936 0.1481 69 T 0.0445 0.6880 0.2675 70 S 0.0479 0.3675 0.5846 71 G 0.0616 0.1204 0.8180 72 I 0.2102 0.1045 0.6854 73 R 0.2749 0.1202 0.6049 74 T 0.1602 0.2516 0.5882 75 D 0.1048 0.2259 0.6693 76 T 0.1167 0.2822 0.6011 77 A 0.1615 0.2999 0.5385 78 T 0.1741 0.3309 0.4950 79 R 0.1999 0.4126 0.3876 80 L 0.1918 0.4223 0.3859 81 E 0.1746 0.4078 0.4176 82 H 0.1529 0.3909 0.4561 83 H 0.1335 0.3019 0.5646 84 H 0.1178 0.2406 0.6416 85 H 0.0978 0.1798 0.7223 86 H 0.0873 0.1072 0.8055 87 H 0.0571 0.0446 0.8982