# This file is the result of combining several RDB files, specifically # T0226.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0226.t2k.stride-ebghtl.rdb (weight 1.24869) # T0226.t2k.str2.rdb (weight 1.54758) # T0226.t2k.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 T0226.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0226 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0226.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 10 # # ============================================ # Comments from T0226.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0226 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0226.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 10 # # ============================================ # Comments from T0226.t2k.str2.rdb # ============================================ # TARGET T0226 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0226.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 10 # # ============================================ # Comments from T0226.t2k.alpha.rdb # ============================================ # TARGET T0226 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0226.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 10 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.0525 0.0665 0.8810 2 L 0.0956 0.2109 0.6936 3 A 0.0761 0.4329 0.4911 4 P 0.0101 0.8818 0.1081 5 Y 0.0070 0.9292 0.0637 6 R 0.0082 0.9354 0.0564 7 Y 0.0082 0.9392 0.0526 8 L 0.0074 0.9386 0.0540 9 R 0.0063 0.9194 0.0743 10 F 0.0061 0.8819 0.1121 11 L 0.0437 0.5108 0.4456 12 L 0.0346 0.1542 0.8112 13 L 0.0796 0.1505 0.7699 14 A 0.1216 0.1501 0.7283 15 T 0.0978 0.0937 0.8085 16 G 0.0769 0.0475 0.8756 17 R 0.0616 0.0406 0.8977 18 E 0.0068 0.8831 0.1100 19 E 0.0054 0.9056 0.0890 20 V 0.0056 0.9294 0.0650 21 L 0.0047 0.9509 0.0443 22 R 0.0048 0.9519 0.0433 23 S 0.0048 0.9508 0.0444 24 V 0.0048 0.9525 0.0427 25 D 0.0047 0.9560 0.0393 26 E 0.0048 0.9474 0.0478 27 A 0.0049 0.9395 0.0555 28 L 0.0053 0.9367 0.0580 29 L 0.0052 0.9298 0.0650 30 E 0.0057 0.9304 0.0639 31 E 0.0068 0.9164 0.0768 32 R 0.0108 0.8806 0.1085 33 R 0.0107 0.8148 0.1745 34 R 0.0192 0.6707 0.3101 35 L 0.0541 0.4400 0.5059 36 G 0.0488 0.1259 0.8253 37 P 0.0749 0.1450 0.7802 38 E 0.1047 0.1646 0.7307 39 V 0.1408 0.0729 0.7863 40 P 0.1286 0.0885 0.7829 41 V 0.0745 0.2510 0.6745 42 E 0.0471 0.2219 0.7309 43 E 0.0362 0.1904 0.7734 44 N 0.0685 0.1243 0.8072 45 P 0.0090 0.8312 0.1598 46 A 0.0059 0.9189 0.0751 47 K 0.0054 0.9434 0.0512 48 F 0.0058 0.9474 0.0467 49 L 0.0057 0.9487 0.0457 50 A 0.0061 0.9467 0.0472 51 Y 0.0059 0.9455 0.0486 52 T 0.0062 0.9279 0.0659 53 L 0.0086 0.8782 0.1132 54 L 0.0203 0.7658 0.2139 55 E 0.0140 0.4975 0.4885 56 R 0.0239 0.3683 0.6077 57 L 0.1047 0.0632 0.8321 58 P 0.1753 0.0442 0.7805 59 L 0.7630 0.0383 0.1986 60 F 0.7997 0.0339 0.1664 61 Y 0.6921 0.0340 0.2739 62 S 0.2504 0.0528 0.6968 63 P 0.0661 0.1414 0.7925 64 L 0.0319 0.2752 0.6929 65 F 0.0266 0.4785 0.4949 66 R 0.0213 0.6477 0.3310 67 P 0.0187 0.7440 0.2372 68 L 0.0108 0.8350 0.1542 69 E 0.0077 0.8915 0.1009 70 G 0.0062 0.8900 0.1038 71 A 0.0052 0.9317 0.0631 72 V 0.0051 0.9454 0.0495 73 Q 0.0048 0.9535 0.0417 74 T 0.0049 0.9524 0.0427 75 L 0.0050 0.9489 0.0460 76 F 0.0050 0.9477 0.0473 77 A 0.0051 0.9306 0.0642 78 R 0.0073 0.8710 0.1217 79 V 0.0117 0.7571 0.2312 80 A 0.0520 0.4834 0.4646 81 K 0.0350 0.1988 0.7662 82 S 0.0716 0.1019 0.8264 83 L 0.0957 0.2628 0.6415 84 S 0.2381 0.2625 0.4995 85 L 0.2976 0.2415 0.4609 86 T 0.1962 0.1970 0.6067 87 P 0.1101 0.1836 0.7062 88 P 0.0975 0.1334 0.7691 89 P 0.0739 0.0869 0.8391 90 S 0.0489 0.1472 0.8039 91 A 0.0583 0.2106 0.7311 92 L 0.1020 0.1593 0.7387 93 E 0.1190 0.1094 0.7717 94 F 0.0928 0.2853 0.6218 95 F 0.1117 0.2989 0.5894 96 L 0.1747 0.3459 0.4794 97 V 0.2160 0.3133 0.4707 98 G 0.1901 0.2651 0.5448 99 L 0.1434 0.2449 0.6117 100 E 0.0975 0.2928 0.6098 101 A 0.0925 0.2601 0.6474 102 R 0.0588 0.3408 0.6004 103 H 0.0512 0.3463 0.6025 104 E 0.0605 0.2545 0.6850 105 Q 0.0881 0.1904 0.7215 106 G 0.0733 0.1622 0.7646 107 D 0.1116 0.1209 0.7675 108 P 0.2420 0.1118 0.6462 109 L 0.5949 0.0425 0.3626 110 A 0.8320 0.0132 0.1548 111 A 0.9025 0.0079 0.0896 112 V 0.9169 0.0050 0.0781 113 L 0.9171 0.0043 0.0786 114 L 0.8753 0.0070 0.1178 115 G 0.6776 0.0094 0.3130 116 P 0.2953 0.0507 0.6541 117 G 0.0650 0.1061 0.8289 118 E 0.0602 0.1200 0.8198 119 E 0.0423 0.2292 0.7285 120 A 0.0305 0.3409 0.6287 121 A 0.0174 0.7795 0.2031 122 L 0.0162 0.8194 0.1645 123 A 0.0117 0.8887 0.0996 124 K 0.0105 0.9270 0.0625 125 E 0.0125 0.9260 0.0615 126 I 0.0102 0.9305 0.0593 127 L 0.0195 0.8943 0.0862 128 E 0.0246 0.8101 0.1652 129 S 0.0444 0.5903 0.3653 130 R 0.0685 0.3812 0.5502 131 V 0.1097 0.3006 0.5897 132 D 0.1519 0.2453 0.6028 133 A 0.2629 0.2050 0.5321 134 L 0.5212 0.1304 0.3484 135 A 0.5628 0.1215 0.3157 136 E 0.6771 0.0675 0.2554 137 V 0.6469 0.0390 0.3141 138 P 0.4931 0.0321 0.4748 139 A 0.2790 0.0462 0.6748 140 T 0.0713 0.0710 0.8577 141 G 0.0469 0.0429 0.9102 142 A 0.0463 0.0596 0.8941 143 N 0.0591 0.1258 0.8151 144 R 0.0120 0.8577 0.1303 145 L 0.0057 0.9215 0.0728 146 A 0.0057 0.9368 0.0575 147 Q 0.0065 0.9415 0.0520 148 V 0.0055 0.9413 0.0532 149 M 0.0057 0.9474 0.0469 150 A 0.0048 0.9517 0.0435 151 L 0.0050 0.9535 0.0415 152 W 0.0048 0.9543 0.0408 153 Y 0.0049 0.9476 0.0475 154 R 0.0049 0.9464 0.0487 155 M 0.0048 0.9566 0.0387 156 A 0.0048 0.9570 0.0382 157 W 0.0047 0.9595 0.0358 158 T 0.0047 0.9607 0.0346 159 A 0.0047 0.9605 0.0348 160 Y 0.0047 0.9602 0.0351 161 Y 0.0047 0.9604 0.0349 162 L 0.0047 0.9605 0.0348 163 A 0.0047 0.9582 0.0371 164 L 0.0050 0.9496 0.0454 165 L 0.0073 0.9094 0.0834 166 Y 0.0448 0.6372 0.3179 167 G 0.0388 0.1857 0.7756 168 V 0.0769 0.0683 0.8548 169 D 0.0909 0.0471 0.8620 170 P 0.0462 0.2545 0.6992 171 G 0.0512 0.2339 0.7148 172 D 0.0757 0.2803 0.6440 173 H 0.0217 0.7488 0.2295 174 G 0.0153 0.8201 0.1645 175 L 0.0112 0.8840 0.1048 176 L 0.0092 0.9152 0.0756 177 E 0.0093 0.9056 0.0851 178 R 0.0093 0.8905 0.1002 179 L 0.0142 0.8665 0.1193 180 R 0.0182 0.8021 0.1798 181 E 0.0265 0.5997 0.3738 182 V 0.0566 0.2848 0.6586 183 T 0.0378 0.0525 0.9098