# This file is the result of combining several RDB files, specifically # T0214.t04.dssp-ebghstl.rdb (weight 1.53986) # T0214.t04.stride-ebghtl.rdb (weight 1.24869) # T0214.t04.str2.rdb (weight 1.54758) # T0214.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 T0214.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0214 # 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 T0214.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 9.63776 # # ============================================ # Comments from T0214.t04.stride-ebghtl.rdb # ============================================ # TARGET T0214 # 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 T0214.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 9.63776 # # ============================================ # Comments from T0214.t04.str2.rdb # ============================================ # TARGET T0214 # 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 T0214.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 9.63776 # # ============================================ # Comments from T0214.t04.alpha.rdb # ============================================ # TARGET T0214 # 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 T0214.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 9.63776 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1849 0.0601 0.7550 2 E 0.4233 0.0922 0.4845 3 W 0.4449 0.1623 0.3928 4 E 0.4342 0.2126 0.3533 5 M 0.3094 0.1820 0.5086 6 G 0.1950 0.1242 0.6807 7 L 0.1509 0.1578 0.6912 8 Q 0.0949 0.2942 0.6109 9 E 0.0232 0.7848 0.1920 10 E 0.0122 0.8918 0.0960 11 F 0.0087 0.9247 0.0666 12 L 0.0109 0.9381 0.0510 13 E 0.0119 0.9432 0.0450 14 L 0.0146 0.9383 0.0471 15 I 0.0279 0.9116 0.0605 16 K 0.0358 0.8467 0.1175 17 L 0.0398 0.3626 0.5976 18 R 0.0528 0.0537 0.8936 19 K 0.1380 0.0224 0.8396 20 K 0.5621 0.0087 0.4292 21 K 0.8387 0.0057 0.1556 22 I 0.8812 0.0055 0.1133 23 E 0.8634 0.0119 0.1246 24 G 0.8238 0.0139 0.1623 25 R 0.7458 0.0201 0.2342 26 L 0.5440 0.0502 0.4057 27 Y 0.3207 0.0757 0.6036 28 D 0.1673 0.1601 0.6726 29 E 0.0355 0.5551 0.4093 30 K 0.0596 0.5827 0.3577 31 R 0.0943 0.6045 0.3012 32 R 0.1406 0.3978 0.4616 33 Q 0.2366 0.1872 0.5762 34 I 0.2362 0.0259 0.7378 35 K 0.0831 0.0176 0.8994 36 P 0.0311 0.0772 0.8917 37 G 0.0383 0.0458 0.9159 38 D 0.2839 0.0240 0.6921 39 V 0.8566 0.0044 0.1390 40 I 0.9195 0.0038 0.0767 41 S 0.9054 0.0050 0.0896 42 F 0.8246 0.0094 0.1660 43 E 0.3252 0.0317 0.6431 44 G 0.0762 0.0268 0.8970 45 G 0.2932 0.0264 0.6805 46 K 0.7223 0.0190 0.2587 47 L 0.8546 0.0062 0.1392 48 K 0.8605 0.0091 0.1304 49 V 0.8811 0.0044 0.1145 50 R 0.8860 0.0049 0.1090 51 V 0.8952 0.0045 0.1003 52 K 0.8402 0.0310 0.1288 53 A 0.8199 0.0184 0.1617 54 I 0.8001 0.0434 0.1565 55 R 0.7788 0.0596 0.1616 56 V 0.7036 0.1065 0.1899 57 Y 0.3995 0.2013 0.3992 58 N 0.1839 0.2801 0.5359 59 S 0.1061 0.3935 0.5004 60 F 0.0110 0.9150 0.0739 61 R 0.0063 0.9527 0.0410 62 E 0.0059 0.9560 0.0380 63 M 0.0055 0.9548 0.0397 64 L 0.0058 0.9413 0.0529 65 E 0.0070 0.9030 0.0900 66 K 0.0112 0.8493 0.1395 67 E 0.0526 0.5617 0.3857 68 G 0.0468 0.1977 0.7555 69 L 0.0563 0.4582 0.4855 70 E 0.0883 0.5315 0.3802 71 N 0.1485 0.4896 0.3619 72 V 0.2652 0.2136 0.5212 73 L 0.1323 0.0550 0.8127 74 P 0.0251 0.0980 0.8768 75 G 0.0224 0.0476 0.9301 76 V 0.1060 0.0531 0.8409 77 K 0.1153 0.1431 0.7416 78 S 0.1589 0.2812 0.5598 79 I 0.0076 0.9280 0.0644 80 E 0.0047 0.9560 0.0394 81 E 0.0047 0.9572 0.0382 82 G 0.0054 0.9528 0.0418 83 I 0.0059 0.9536 0.0405 84 Q 0.0075 0.9523 0.0402 85 V 0.0098 0.9423 0.0480 86 Y 0.0131 0.9134 0.0735 87 R 0.0158 0.8938 0.0904 88 R 0.0200 0.8256 0.1545 89 F 0.0368 0.6601 0.3032 90 Y 0.1122 0.2765 0.6113 91 D 0.0609 0.0690 0.8701 92 E 0.0050 0.8672 0.1278 93 E 0.0081 0.8387 0.1532 94 K 0.0205 0.8452 0.1343 95 E 0.0468 0.7813 0.1719 96 K 0.0697 0.6536 0.2767 97 K 0.1494 0.4060 0.4446 98 Y 0.2194 0.1090 0.6716 99 G 0.4149 0.0273 0.5577 100 V 0.8254 0.0071 0.1675 101 V 0.8996 0.0076 0.0928 102 A 0.9140 0.0047 0.0813 103 I 0.9037 0.0044 0.0919 104 E 0.8965 0.0039 0.0996 105 I 0.8485 0.0066 0.1449 106 E 0.7446 0.0090 0.2464 107 P 0.6770 0.0150 0.3080 108 L 0.3444 0.0516 0.6040 109 E 0.2329 0.0457 0.7214 110 Y 0.0994 0.0400 0.8606