# This file is the result of combining several RDB files, specifically # T0309.t04.dssp-ebghstl.rdb (weight 1.53986) # T0309.t04.stride-ebghtl.rdb (weight 1.24869) # T0309.t04.str2.rdb (weight 1.54758) # T0309.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 T0309.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t04.stride-ebghtl.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t04.str2.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t04.alpha.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0727 0.2258 0.7015 2 A 0.0978 0.2465 0.6557 3 S 0.1092 0.2524 0.6384 4 K 0.1447 0.2513 0.6040 5 K 0.2873 0.1915 0.5212 6 V 0.4277 0.1598 0.4125 7 H 0.5137 0.1254 0.3609 8 Q 0.6802 0.1004 0.2194 9 I 0.6932 0.0883 0.2185 10 N 0.6032 0.0648 0.3320 11 V 0.5331 0.0827 0.3842 12 K 0.3624 0.1215 0.5161 13 G 0.3519 0.0847 0.5635 14 F 0.4604 0.0997 0.4399 15 F 0.5137 0.0757 0.4106 16 D 0.4348 0.0666 0.4986 17 M 0.3105 0.1301 0.5594 18 D 0.3480 0.1440 0.5080 19 V 0.4612 0.2233 0.3154 20 M 0.5676 0.1675 0.2649 21 E 0.6171 0.1630 0.2199 22 V 0.5377 0.1477 0.3146 23 T 0.4045 0.1394 0.4561 24 E 0.2386 0.3089 0.4525 25 Q 0.2144 0.2768 0.5087 26 T 0.2113 0.1761 0.6126 27 K 0.2219 0.2716 0.5064 28 E 0.3340 0.2524 0.4136 29 A 0.3979 0.2362 0.3659 30 E 0.4451 0.2337 0.3212 31 Y 0.4978 0.1700 0.3322 32 T 0.4591 0.1768 0.3641 33 Y 0.3405 0.1979 0.4616 34 D 0.2413 0.2190 0.5396 35 F 0.0220 0.8823 0.0957 36 K 0.0136 0.9247 0.0618 37 E 0.0208 0.9201 0.0591 38 I 0.0268 0.9048 0.0684 39 L 0.0230 0.8899 0.0871 40 S 0.0193 0.8310 0.1497 41 E 0.0212 0.7475 0.2313 42 F 0.0668 0.5166 0.4165 43 N 0.0650 0.1540 0.7809 44 G 0.0434 0.0562 0.9004 45 K 0.1322 0.0510 0.8169 46 N 0.3222 0.0267 0.6511 47 V 0.5720 0.0125 0.4156 48 S 0.7921 0.0063 0.2016 49 I 0.8625 0.0047 0.1328 50 T 0.8565 0.0064 0.1371 51 V 0.8270 0.0090 0.1639 52 K 0.6947 0.0225 0.2828 53 E 0.6437 0.0495 0.3068 54 E 0.3861 0.1303 0.4836 55 N 0.2767 0.0928 0.6305 56 E 0.3541 0.0571 0.5888 57 L 0.4444 0.0191 0.5365 58 P 0.4100 0.0238 0.5663 59 V 0.4701 0.0557 0.4742 60 K 0.3444 0.0964 0.5592 61 G 0.3723 0.0779 0.5499 62 V 0.6000 0.0720 0.3280 63 E 0.7157 0.0541 0.2302 64 M 0.5846 0.0632 0.3522 65 A 0.2477 0.0828 0.6695 66 G 0.0852 0.0501 0.8647 67 D 0.1179 0.0261 0.8561 68 P 0.0872 0.2091 0.7038 69 L 0.0807 0.3411 0.5782 70 E 0.1003 0.3952 0.5045 71 H 0.1261 0.3573 0.5166 72 H 0.1468 0.2773 0.5759 73 H 0.1394 0.2130 0.6477 74 H 0.1173 0.1715 0.7112 75 H 0.0969 0.1035 0.7996 76 H 0.0590 0.0424 0.8986