# This file is the result of combining several RDB files, specifically # T0289.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0289.t2k.stride-ebghtl.rdb (weight 1.24869) # T0289.t2k.str2.rdb (weight 1.54758) # T0289.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 T0289.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 48 # # ============================================ # Comments from T0289.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 48 # # ============================================ # Comments from T0289.t2k.str2.rdb # ============================================ # TARGET T0289 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0289.t2k-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 13.2251 # # ============================================ # Comments from T0289.t2k.alpha.rdb # ============================================ # TARGET T0289 # 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 T0289.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 48 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0257 0.5382 0.4361 2 L 0.0119 0.8712 0.1169 3 D 0.0171 0.8980 0.0849 4 F 0.0196 0.9113 0.0691 5 I 0.0204 0.9008 0.0788 6 Q 0.0239 0.9025 0.0736 7 R 0.0298 0.8791 0.0910 8 F 0.0267 0.8169 0.1564 9 N 0.0351 0.6424 0.3225 10 E 0.0503 0.2705 0.6792 11 G 0.0349 0.0589 0.9062 12 K 0.0967 0.0335 0.8697 13 E 0.2327 0.0231 0.7442 14 F 0.1365 0.0253 0.8382 15 P 0.1111 0.0320 0.8569 16 P 0.0934 0.1236 0.7830 17 C 0.0949 0.1615 0.7436 18 A 0.3625 0.1159 0.5216 19 I 0.7421 0.0180 0.2399 20 D 0.8588 0.0149 0.1263 21 V 0.8823 0.0139 0.1039 22 Y 0.8517 0.0231 0.1252 23 K 0.8009 0.0353 0.1638 24 I 0.6551 0.0590 0.2859 25 M 0.4537 0.0977 0.4486 26 E 0.3656 0.1040 0.5304 27 K 0.3835 0.0660 0.5505 28 V 0.4439 0.0227 0.5334 29 D 0.3719 0.0228 0.6053 30 Y 0.3721 0.0163 0.6116 31 P 0.3379 0.0211 0.6411 32 R 0.4302 0.0327 0.5371 33 N 0.1168 0.0267 0.8565 34 E 0.0274 0.1181 0.8545 35 S 0.0510 0.0211 0.9279 36 G 0.0522 0.0267 0.9211 37 D 0.2352 0.0147 0.7501 38 V 0.7647 0.0061 0.2293 39 A 0.7936 0.0192 0.1873 40 A 0.8640 0.0146 0.1215 41 V 0.8803 0.0150 0.1047 42 I 0.8174 0.0139 0.1686 43 H 0.5309 0.0161 0.4530 44 P 0.1139 0.3546 0.5315 45 N 0.0571 0.3701 0.5728 46 L 0.0973 0.3676 0.5351 47 Q 0.1528 0.1772 0.6700 48 D 0.0976 0.1469 0.7555 49 Q 0.1016 0.1779 0.7204 50 D 0.1562 0.1448 0.6990 51 W 0.1985 0.2347 0.5668 52 K 0.2155 0.1556 0.6288 53 P 0.3433 0.1133 0.5434 54 L 0.2613 0.0681 0.6706 55 H 0.0808 0.0289 0.8903 56 P 0.0275 0.0684 0.9041 57 G 0.0210 0.0414 0.9377 58 D 0.0915 0.0208 0.8876 59 P 0.3735 0.0292 0.5973 60 V 0.6094 0.0665 0.3242 61 F 0.7625 0.0437 0.1937 62 V 0.7960 0.0283 0.1757 63 S 0.6020 0.0350 0.3630 64 L 0.3151 0.0707 0.6142 65 D 0.0768 0.0392 0.8840 66 G 0.0550 0.0510 0.8940 67 K 0.3595 0.0230 0.6175 68 V 0.8010 0.0084 0.1907 69 I 0.7941 0.0093 0.1966 70 P 0.7366 0.0147 0.2487 71 L 0.4830 0.0461 0.4709 72 G 0.1586 0.0736 0.7678 73 G 0.0739 0.0680 0.8581 74 D 0.1142 0.0644 0.8215 75 C 0.2111 0.0378 0.7510 76 T 0.4241 0.0293 0.5467 77 V 0.6208 0.0245 0.3547 78 Y 0.6452 0.0214 0.3334 79 P 0.6900 0.0368 0.2733 80 V 0.8082 0.0591 0.1327 81 F 0.8098 0.0699 0.1204 82 V 0.6417 0.1824 0.1759 83 N 0.3754 0.2694 0.3551 84 E 0.1600 0.5420 0.2980 85 A 0.0934 0.7387 0.1679 86 A 0.0899 0.7731 0.1369 87 Y 0.0952 0.7738 0.1310 88 Y 0.1070 0.7421 0.1509 89 E 0.0956 0.7112 0.1932 90 K 0.0522 0.5487 0.3991 91 K 0.0433 0.3752 0.5815 92 E 0.1353 0.4294 0.4353 93 A 0.3095 0.3865 0.3040 94 F 0.3988 0.3328 0.2684 95 A 0.5494 0.2327 0.2180 96 K 0.5449 0.2031 0.2520 97 T 0.6052 0.1037 0.2911 98 T 0.6172 0.0698 0.3130 99 K 0.6409 0.0563 0.3028 100 L 0.7058 0.0441 0.2501 101 T 0.7116 0.0344 0.2540 102 L 0.6709 0.0204 0.3087 103 N 0.5611 0.0273 0.4116 104 A 0.3145 0.1521 0.5334 105 K 0.1909 0.2511 0.5580 106 S 0.2270 0.3421 0.4309 107 I 0.3343 0.3509 0.3149 108 R 0.3541 0.2999 0.3460 109 S 0.2817 0.2866 0.4317 110 T 0.2028 0.2076 0.5896 111 L 0.1350 0.1301 0.7349 112 H 0.0595 0.0477 0.8928