# This file is the result of combining several RDB files, specifically # T0300.t04.dssp-ebghstl.rdb (weight 1.53986) # T0300.t04.stride-ebghtl.rdb (weight 1.24869) # T0300.t04.str2.rdb (weight 1.54758) # T0300.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 T0300.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0300 # 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 T0300.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 8.88843 # # ============================================ # Comments from T0300.t04.stride-ebghtl.rdb # ============================================ # TARGET T0300 # 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 T0300.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 8.88843 # # ============================================ # Comments from T0300.t04.str2.rdb # ============================================ # TARGET T0300 # 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 T0300.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 8.88843 # # ============================================ # Comments from T0300.t04.alpha.rdb # ============================================ # TARGET T0300 # 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 T0300.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 8.88843 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0588 0.0389 0.9024 2 A 0.0635 0.1144 0.8221 3 S 0.0591 0.1143 0.8266 4 K 0.0616 0.0864 0.8521 5 K 0.0610 0.0260 0.9130 6 P 0.0492 0.0685 0.8824 7 D 0.0709 0.0437 0.8855 8 K 0.1017 0.0320 0.8663 9 T 0.0994 0.0287 0.8719 10 Y 0.0047 0.9533 0.0420 11 E 0.0047 0.9612 0.0342 12 E 0.0046 0.9608 0.0346 13 M 0.0047 0.9600 0.0353 14 V 0.0047 0.9605 0.0348 15 K 0.0046 0.9599 0.0355 16 E 0.0047 0.9586 0.0367 17 V 0.0047 0.9594 0.0359 18 E 0.0047 0.9575 0.0378 19 R 0.0047 0.9513 0.0440 20 L 0.0049 0.9506 0.0446 21 K 0.0052 0.9500 0.0448 22 L 0.0051 0.9473 0.0476 23 E 0.0062 0.9342 0.0596 24 N 0.0166 0.9126 0.0708 25 K 0.0047 0.9517 0.0436 26 T 0.0047 0.9497 0.0456 27 L 0.0047 0.9514 0.0439 28 K 0.0047 0.9526 0.0427 29 Q 0.0053 0.9464 0.0482 30 K 0.0061 0.9412 0.0527 31 V 0.0129 0.9026 0.0846 32 K 0.0190 0.8175 0.1635 33 S 0.0250 0.6312 0.3437 34 S 0.0562 0.2589 0.6849 35 G 0.0462 0.0757 0.8781 36 A 0.0986 0.0533 0.8481 37 V 0.1526 0.0329 0.8145 38 S 0.0866 0.0219 0.8915 39 S 0.0532 0.0985 0.8483 40 D 0.0429 0.1353 0.8218 41 D 0.0558 0.1993 0.7450 42 S 0.1179 0.1899 0.6922 43 I 0.2540 0.1212 0.6248 44 L 0.2305 0.0481 0.7214 45 T 0.0846 0.0256 0.8898 46 A 0.0070 0.8939 0.0991 47 A 0.0061 0.9240 0.0699 48 K 0.0059 0.9343 0.0599 49 R 0.0077 0.9347 0.0577 50 E 0.0163 0.9211 0.0626 51 S 0.0215 0.9211 0.0574 52 I 0.0186 0.9303 0.0511 53 I 0.0224 0.9174 0.0602 54 V 0.0149 0.9125 0.0726 55 S 0.0137 0.8863 0.1000 56 S 0.0091 0.8870 0.1040 57 S 0.0083 0.8967 0.0949 58 R 0.0063 0.8978 0.0959 59 A 0.0054 0.9052 0.0894 60 L 0.0050 0.9134 0.0816 61 G 0.0049 0.9311 0.0641 62 A 0.0047 0.9573 0.0380 63 V 0.0047 0.9589 0.0365 64 A 0.0047 0.9577 0.0376 65 M 0.0047 0.9596 0.0358 66 R 0.0046 0.9608 0.0346 67 K 0.0046 0.9608 0.0346 68 I 0.0047 0.9599 0.0354 69 E 0.0047 0.9599 0.0354 70 A 0.0047 0.9588 0.0365 71 K 0.0047 0.9568 0.0385 72 V 0.0048 0.9492 0.0461 73 R 0.0057 0.9240 0.0702 74 S 0.0078 0.8728 0.1194 75 R 0.0110 0.7821 0.2069 76 A 0.0281 0.6723 0.2996 77 A 0.0374 0.5105 0.4521 78 K 0.0572 0.3941 0.5487 79 A 0.0847 0.1952 0.7201 80 V 0.1462 0.1032 0.7506 81 T 0.0763 0.0447 0.8790 82 E 0.0049 0.9488 0.0464 83 Q 0.0047 0.9559 0.0394 84 E 0.0047 0.9570 0.0382 85 L 0.0047 0.9590 0.0363 86 T 0.0047 0.9593 0.0360 87 S 0.0048 0.9538 0.0414 88 L 0.0052 0.9438 0.0510 89 L 0.0128 0.8851 0.1021 90 Q 0.0155 0.6474 0.3371 91 S 0.0424 0.2879 0.6697 92 L 0.1709 0.0412 0.7879 93 T 0.3727 0.0291 0.5982 94 L 0.8648 0.0054 0.1298 95 R 0.9129 0.0034 0.0837 96 V 0.9020 0.0034 0.0946 97 D 0.8789 0.0034 0.1176 98 V 0.7560 0.0055 0.2385 99 S 0.5549 0.0090 0.4361 100 M 0.2598 0.0741 0.6661 101 E 0.1219 0.0637 0.8144 102 E 0.0630 0.0764 0.8606