# This file is the result of combining several RDB files, specifically # T0207.t04.dssp-ebghstl.rdb (weight 1.53986) # T0207.t04.stride-ebghtl.rdb (weight 1.24869) # T0207.t04.str2.rdb (weight 1.54758) # T0207.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 T0207.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0207 # 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 T0207.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 215 # # ============================================ # Comments from T0207.t04.stride-ebghtl.rdb # ============================================ # TARGET T0207 # 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 T0207.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 215 # # ============================================ # Comments from T0207.t04.str2.rdb # ============================================ # TARGET T0207 # 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 T0207.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 215 # # ============================================ # Comments from T0207.t04.alpha.rdb # ============================================ # TARGET T0207 # 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 T0207.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 215 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1712 0.0079 0.8209 2 A 0.7871 0.0046 0.2084 3 L 0.9124 0.0035 0.0842 4 T 0.9270 0.0035 0.0695 5 L 0.9199 0.0037 0.0763 6 Y 0.8333 0.0107 0.1560 7 Q 0.4978 0.0100 0.4922 8 R 0.1530 0.0368 0.8102 9 D 0.0396 0.1050 0.8554 10 D 0.0336 0.1170 0.8494 11 C 0.0693 0.1478 0.7829 12 H 0.0656 0.3621 0.5722 13 L 0.0460 0.5291 0.4249 14 C 0.0134 0.7934 0.1932 15 D 0.0050 0.9405 0.0546 16 Q 0.0048 0.9512 0.0440 17 A 0.0048 0.9538 0.0414 18 V 0.0047 0.9596 0.0357 19 E 0.0047 0.9604 0.0350 20 A 0.0047 0.9605 0.0349 21 L 0.0047 0.9559 0.0394 22 A 0.0048 0.9333 0.0619 23 Q 0.0054 0.8651 0.1295 24 A 0.0290 0.5525 0.4185 25 R 0.0306 0.1521 0.8172 26 A 0.0686 0.0614 0.8701 27 G 0.1206 0.0569 0.8225 28 A 0.5333 0.0197 0.4470 29 F 0.7983 0.0062 0.1955 30 F 0.8935 0.0045 0.1021 31 S 0.9049 0.0040 0.0911 32 V 0.8700 0.0056 0.1245 33 F 0.7834 0.0058 0.2108 34 I 0.3993 0.0541 0.5466 35 D 0.1639 0.0491 0.7870 36 D 0.0538 0.0795 0.8667 37 D 0.0921 0.0690 0.8389 38 A 0.0057 0.8980 0.0963 39 A 0.0052 0.9362 0.0586 40 L 0.0052 0.9414 0.0534 41 E 0.0081 0.9263 0.0656 42 S 0.0073 0.8746 0.1181 43 A 0.0139 0.7421 0.2440 44 Y 0.0543 0.3180 0.6277 45 G 0.0517 0.0414 0.9069 46 L 0.2268 0.0164 0.7568 47 R 0.4208 0.0213 0.5579 48 V 0.6269 0.0067 0.3663 49 P 0.6998 0.0059 0.2943 50 V 0.8824 0.0054 0.1123 51 L 0.8847 0.0050 0.1103 52 R 0.7854 0.0110 0.2037 53 D 0.4743 0.0166 0.5091 54 P 0.0840 0.0691 0.8470 55 M 0.0607 0.0459 0.8934 56 G 0.1643 0.0464 0.7893 57 R 0.4909 0.0346 0.4745 58 E 0.7304 0.0276 0.2420 59 L 0.5939 0.0457 0.3604 60 D 0.2905 0.0474 0.6620 61 W 0.1758 0.0451 0.7791 62 P 0.1431 0.0588 0.7982 63 F 0.1290 0.0382 0.8328 64 D 0.0805 0.0234 0.8961 65 A 0.0064 0.8977 0.0959 66 P 0.0047 0.9494 0.0459 67 R 0.0048 0.9526 0.0427 68 L 0.0048 0.9554 0.0398 69 R 0.0047 0.9561 0.0392 70 A 0.0048 0.9500 0.0452 71 W 0.0051 0.9396 0.0553 72 L 0.0069 0.9037 0.0895 73 D 0.0070 0.7955 0.1975 74 A 0.0134 0.5531 0.4335 75 A 0.0540 0.1715 0.7745 76 P 0.0271 0.1843 0.7887 77 H 0.0339 0.1352 0.8309 78 A 0.0395 0.0694 0.8910