# This file is the result of combining several RDB files, specifically # T0235.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0235.t2k.stride-ebghtl.rdb (weight 1.24869) # T0235.t2k.str2.rdb (weight 1.54758) # T0235.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 T0235.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0235 # 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 T0235.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 4 # # ============================================ # Comments from T0235.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0235 # 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 T0235.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 4 # # ============================================ # Comments from T0235.t2k.str2.rdb # ============================================ # TARGET T0235 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0235.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 4 # # ============================================ # Comments from T0235.t2k.alpha.rdb # ============================================ # TARGET T0235 # 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 T0235.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 4 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.0613 0.1458 0.7929 2 E 0.0884 0.4179 0.4938 3 Y 0.1080 0.4481 0.4439 4 A 0.0949 0.5414 0.3637 5 A 0.1042 0.5613 0.3345 6 E 0.1241 0.6041 0.2717 7 K 0.1405 0.6538 0.2057 8 V 0.1716 0.6408 0.1877 9 K 0.1660 0.6507 0.1833 10 V 0.0695 0.7610 0.1695 11 R 0.0268 0.8389 0.1343 12 D 0.0150 0.8923 0.0927 13 E 0.0076 0.9151 0.0774 14 L 0.0096 0.8929 0.0976 15 R 0.0159 0.8602 0.1239 16 K 0.0160 0.8397 0.1443 17 V 0.0193 0.7809 0.1998 18 E 0.0252 0.7757 0.1991 19 K 0.0144 0.7754 0.2102 20 E 0.0184 0.7425 0.2391 21 K 0.0182 0.7019 0.2799 22 N 0.0189 0.6894 0.2917 23 E 0.0212 0.6970 0.2818 24 K 0.0155 0.7204 0.2640 25 E 0.0125 0.7690 0.2185 26 R 0.0142 0.8164 0.1694 27 E 0.0165 0.8077 0.1758 28 I 0.0196 0.8043 0.1761 29 K 0.0272 0.7344 0.2384 30 R 0.0363 0.5866 0.3771 31 R 0.0598 0.4178 0.5224 32 K 0.0955 0.3017 0.6028 33 F 0.1484 0.1826 0.6690 34 D 0.1240 0.1130 0.7630 35 P 0.1390 0.1448 0.7162 36 S 0.1387 0.0962 0.7651 37 S 0.1082 0.0960 0.7958 38 S 0.0787 0.1761 0.7452 39 E 0.0479 0.1857 0.7664 40 N 0.0474 0.1402 0.8124 41 V 0.0930 0.0718 0.8351 42 M 0.1303 0.0628 0.8069 43 T 0.0736 0.0750 0.8513 44 P 0.0208 0.7162 0.2630 45 R 0.0084 0.8427 0.1489 46 E 0.0072 0.8818 0.1110 47 Q 0.0066 0.9228 0.0706 48 Y 0.0067 0.9303 0.0630 49 E 0.0062 0.9364 0.0574 50 T 0.0055 0.9391 0.0554 51 Q 0.0058 0.9359 0.0583 52 V 0.0063 0.9166 0.0772 53 A 0.0062 0.8915 0.1023 54 L 0.0102 0.8184 0.1713 55 N 0.0128 0.6995 0.2877 56 E 0.0145 0.6566 0.3289 57 S 0.0230 0.4818 0.4952 58 E 0.0123 0.6628 0.3250 59 K 0.0094 0.7725 0.2181 60 D 0.0073 0.8799 0.1128 61 Q 0.0062 0.9096 0.0842 62 W 0.0066 0.9200 0.0734 63 L 0.0057 0.9353 0.0590 64 E 0.0056 0.9380 0.0565 65 E 0.0051 0.9367 0.0582 66 Y 0.0058 0.9253 0.0690 67 K 0.0061 0.8993 0.0946 68 K 0.0087 0.8273 0.1640 69 H 0.0169 0.6515 0.3316 70 F 0.0533 0.1631 0.7835 71 P 0.0361 0.2127 0.7511 72 P 0.0198 0.4239 0.5562 73 N 0.0450 0.4121 0.5429 74 L 0.0389 0.4073 0.5538 75 E 0.0501 0.2995 0.6504 76 K 0.0534 0.2715 0.6751 77 G 0.0520 0.1920 0.7560 78 E 0.0863 0.1470 0.7667 79 N 0.0784 0.0840 0.8377 80 P 0.0369 0.0722 0.8909