# This file is the result of combining several RDB files, specifically # T0340.t06.dssp-ebghstl.rdb (weight 1.53986) # T0340.t06.stride-ebghtl.rdb (weight 1.24869) # T0340.t06.str2.rdb (weight 1.54758) # T0340.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 T0340.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1995 # # ============================================ # Comments from T0340.t06.stride-ebghtl.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1995 # # ============================================ # Comments from T0340.t06.str2.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1995 # # ============================================ # Comments from T0340.t06.alpha.rdb # ============================================ # TARGET T0340 # 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 T0340.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 1995 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0625 0.0269 0.9106 2 M 0.0896 0.0479 0.8624 3 L 0.1171 0.0414 0.8415 4 R 0.2237 0.0168 0.7595 5 P 0.3816 0.0087 0.6097 6 R 0.7408 0.0067 0.2525 7 L 0.9104 0.0032 0.0864 8 C 0.9163 0.0035 0.0802 9 H 0.9148 0.0034 0.0818 10 L 0.8872 0.0038 0.1090 11 R 0.7498 0.0067 0.2435 12 K 0.5547 0.0228 0.4224 13 G 0.1985 0.0176 0.7839 14 P 0.0821 0.0710 0.8469 15 Q 0.0729 0.0703 0.8568 16 G 0.1918 0.0545 0.7537 17 Y 0.4233 0.0271 0.5495 18 G 0.7980 0.0112 0.1908 19 F 0.8929 0.0042 0.1029 20 N 0.9086 0.0042 0.0872 21 L 0.9053 0.0039 0.0908 22 H 0.8169 0.0160 0.1671 23 S 0.5838 0.0193 0.3969 24 D 0.2283 0.0377 0.7341 25 K 0.1700 0.0602 0.7698 26 S 0.1131 0.0577 0.8292 27 R 0.1144 0.0358 0.8498 28 P 0.1383 0.0513 0.8104 29 G 0.4168 0.0309 0.5522 30 Q 0.7654 0.0074 0.2272 31 Y 0.8880 0.0050 0.1070 32 I 0.8872 0.0041 0.1086 33 R 0.8083 0.0342 0.1575 34 S 0.7944 0.0060 0.1996 35 V 0.5601 0.0092 0.4307 36 D 0.1599 0.0158 0.8243 37 P 0.0315 0.0752 0.8932 38 G 0.0263 0.0505 0.9232 39 S 0.0929 0.0522 0.8548 40 P 0.0470 0.6481 0.3049 41 A 0.0228 0.7538 0.2234 42 A 0.0243 0.7760 0.1996 43 R 0.0269 0.7207 0.2524 44 S 0.0477 0.2952 0.6571 45 G 0.0409 0.0603 0.8989 46 L 0.1139 0.0153 0.8708 47 R 0.1107 0.0227 0.8666 48 A 0.0388 0.1913 0.7699 49 Q 0.0606 0.0998 0.8396 50 D 0.2795 0.0751 0.6454 51 R 0.7522 0.0199 0.2279 52 L 0.8866 0.0161 0.0973 53 I 0.8531 0.0203 0.1266 54 E 0.8961 0.0126 0.0912 55 V 0.8156 0.0266 0.1578 56 N 0.3018 0.0426 0.6556 57 G 0.1273 0.0362 0.8365 58 Q 0.6357 0.0142 0.3501 59 N 0.6839 0.0124 0.3036 60 V 0.2812 0.1755 0.5433 61 E 0.0691 0.1714 0.7594 62 G 0.0533 0.0910 0.8557 63 L 0.1996 0.0175 0.7829 64 R 0.1923 0.0158 0.7919 65 H 0.0056 0.9316 0.0627 66 A 0.0047 0.9583 0.0370 67 E 0.0047 0.9601 0.0352 68 V 0.0047 0.9606 0.0347 69 V 0.0047 0.9600 0.0353 70 A 0.0047 0.9585 0.0368 71 S 0.0050 0.9519 0.0431 72 I 0.0072 0.9312 0.0616 73 K 0.0093 0.8456 0.1451 74 A 0.0171 0.5521 0.4308 75 R 0.0652 0.1237 0.8111 76 E 0.0327 0.0898 0.8776 77 D 0.0651 0.0682 0.8668 78 E 0.4804 0.0216 0.4980 79 A 0.8516 0.0044 0.1439 80 R 0.9210 0.0034 0.0755 81 L 0.9300 0.0033 0.0667 82 L 0.9244 0.0036 0.0720 83 V 0.9161 0.0038 0.0801 84 V 0.7421 0.0145 0.2434 85 G 0.3258 0.0101 0.6642 86 P 0.0938 0.0401 0.8661 87 S 0.0846 0.0435 0.8719 88 T 0.1005 0.0658 0.8337 89 R 0.1058 0.0487 0.8455 90 L 0.0589 0.0345 0.9066