# This file is the result of combining several RDB files, specifically # T0215.t04.dssp-ebghstl.rdb (weight 1.53986) # T0215.t04.stride-ebghtl.rdb (weight 1.24869) # T0215.t04.str2.rdb (weight 1.54758) # T0215.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 T0215.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0215 # Using neural net t04-2621-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 T0215.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 3.42992 # # ============================================ # Comments from T0215.t04.stride-ebghtl.rdb # ============================================ # TARGET T0215 # 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 T0215.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 3.42992 # # ============================================ # Comments from T0215.t04.str2.rdb # ============================================ # TARGET T0215 # 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 T0215.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 3.42992 # # ============================================ # Comments from T0215.t04.alpha.rdb # ============================================ # TARGET T0215 # 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 T0215.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 3.42992 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1211 0.0752 0.8038 2 G 0.1383 0.0583 0.8035 3 T 0.2228 0.1338 0.6434 4 S 0.4505 0.1321 0.4174 5 H 0.6432 0.1333 0.2235 6 H 0.7165 0.1212 0.1623 7 H 0.6971 0.1386 0.1644 8 H 0.6422 0.1612 0.1966 9 H 0.5716 0.1671 0.2613 10 H 0.4090 0.2216 0.3693 11 S 0.2885 0.2202 0.4914 12 S 0.2364 0.2156 0.5480 13 G 0.1739 0.3831 0.4430 14 R 0.2290 0.4865 0.2845 15 E 0.2815 0.4839 0.2346 16 N 0.3721 0.4526 0.1753 17 L 0.5155 0.3248 0.1597 18 Y 0.5640 0.2669 0.1691 19 F 0.4614 0.2631 0.2755 20 Q 0.2536 0.3070 0.4393 21 G 0.1656 0.3001 0.5343 22 H 0.1478 0.3153 0.5369 23 M 0.1513 0.2526 0.5961 24 R 0.0890 0.1879 0.7232 25 N 0.0816 0.1080 0.8104 26 L 0.0829 0.3718 0.5453 27 S 0.1067 0.4227 0.4706 28 D 0.1265 0.4528 0.4207 29 R 0.0737 0.6093 0.3170 30 A 0.1063 0.6123 0.2814 31 K 0.1113 0.6301 0.2586 32 F 0.0629 0.7559 0.1813 33 E 0.0526 0.7893 0.1582 34 S 0.0618 0.7565 0.1817 35 M 0.0745 0.7076 0.2179 36 I 0.1319 0.4675 0.4005 37 N 0.1013 0.1972 0.7014 38 S 0.0832 0.1014 0.8155 39 P 0.0278 0.2508 0.7213 40 S 0.0585 0.2838 0.6577 41 K 0.0351 0.6579 0.3069 42 S 0.0652 0.7252 0.2096 43 V 0.1663 0.6883 0.1454 44 F 0.2327 0.6592 0.1081 45 V 0.1953 0.6728 0.1320 46 R 0.1432 0.5932 0.2636 47 N 0.0759 0.4555 0.4687 48 L 0.0060 0.8790 0.1150 49 N 0.0049 0.9374 0.0577 50 E 0.0047 0.9533 0.0420 51 L 0.0047 0.9566 0.0387 52 E 0.0047 0.9607 0.0346 53 A 0.0046 0.9612 0.0341 54 L 0.0047 0.9600 0.0353 55 A 0.0047 0.9574 0.0379 56 V 0.0049 0.9500 0.0451 57 R 0.0061 0.9279 0.0660 58 L 0.0407 0.7251 0.2342 59 G 0.0255 0.2264 0.7481 60 K 0.0350 0.4307 0.5343 61 S 0.0554 0.5937 0.3509 62 Y 0.0502 0.7953 0.1545 63 R 0.0612 0.8258 0.1131 64 I 0.0740 0.8138 0.1122 65 Q 0.0599 0.7986 0.1415 66 L 0.0158 0.8870 0.0972 67 D 0.0089 0.8965 0.0946 68 Q 0.0081 0.8878 0.1041 69 A 0.0141 0.8238 0.1621 70 K 0.0214 0.6982 0.2804 71 E 0.0304 0.6066 0.3630 72 K 0.0640 0.5485 0.3875 73 W 0.1818 0.2978 0.5204 74 K 0.2964 0.1983 0.5054 75 V 0.2131 0.0791 0.7079 76 K 0.0760 0.0534 0.8706