# This file is the result of combining several RDB files, specifically # T0309.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0309.t2k.stride-ebghtl.rdb (weight 1.24869) # T0309.t2k.str2.rdb (weight 1.54758) # T0309.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 T0309.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0309 # 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 T0309.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 1 # # ============================================ # Comments from T0309.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0309 # 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 T0309.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 1 # # ============================================ # Comments from T0309.t2k.str2.rdb # ============================================ # TARGET T0309 # 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 T0309.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 1 # # ============================================ # Comments from T0309.t2k.alpha.rdb # ============================================ # TARGET T0309 # 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 T0309.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0700 0.0923 0.8377 2 A 0.1057 0.1172 0.7772 3 S 0.1180 0.1249 0.7571 4 K 0.1569 0.1936 0.6496 5 K 0.2502 0.1853 0.5644 6 V 0.3606 0.1541 0.4854 7 H 0.4422 0.1374 0.4204 8 Q 0.6035 0.0884 0.3081 9 I 0.6174 0.0690 0.3136 10 N 0.5697 0.0572 0.3731 11 V 0.4466 0.1135 0.4399 12 K 0.2663 0.1638 0.5698 13 G 0.2401 0.1560 0.6039 14 F 0.4138 0.1270 0.4592 15 F 0.4641 0.0963 0.4396 16 D 0.3796 0.0874 0.5330 17 M 0.3061 0.1954 0.4985 18 D 0.3819 0.1972 0.4210 19 V 0.4900 0.2202 0.2898 20 M 0.5252 0.2187 0.2561 21 E 0.5707 0.1908 0.2385 22 V 0.4215 0.2591 0.3194 23 T 0.2958 0.2854 0.4188 24 E 0.1914 0.3946 0.4139 25 Q 0.1466 0.4095 0.4439 26 T 0.1372 0.3420 0.5208 27 K 0.1008 0.4231 0.4761 28 E 0.1034 0.4943 0.4024 29 A 0.0959 0.4913 0.4128 30 E 0.1499 0.4192 0.4309 31 Y 0.1991 0.3892 0.4117 32 T 0.1865 0.3624 0.4512 33 Y 0.1452 0.4168 0.4381 34 D 0.1329 0.4028 0.4643 35 F 0.0260 0.8717 0.1023 36 K 0.0162 0.9047 0.0791 37 E 0.0209 0.9008 0.0783 38 I 0.0233 0.8941 0.0826 39 L 0.0283 0.8600 0.1117 40 S 0.0344 0.8107 0.1549 41 E 0.0354 0.7161 0.2484 42 F 0.0756 0.4181 0.5064 43 N 0.0615 0.1575 0.7810 44 G 0.0599 0.0920 0.8481 45 K 0.1524 0.0880 0.7597 46 N 0.4388 0.0385 0.5227 47 V 0.6248 0.0223 0.3530 48 S 0.7500 0.0146 0.2354 49 I 0.8206 0.0156 0.1638 50 T 0.8316 0.0141 0.1543 51 V 0.7407 0.0314 0.2279 52 K 0.6117 0.0563 0.3320 53 E 0.4146 0.1188 0.4666 54 E 0.2490 0.1984 0.5526 55 N 0.2002 0.1517 0.6481 56 E 0.2175 0.1211 0.6614 57 L 0.2222 0.0528 0.7249 58 P 0.2272 0.0675 0.7053 59 V 0.2304 0.1519 0.6177 60 K 0.1501 0.2090 0.6409 61 G 0.1449 0.1240 0.7311 62 V 0.1660 0.0687 0.7653 63 E 0.0595 0.0429 0.8975