# This file is the result of combining several RDB files, specifically # T0361.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0361.t2k.stride-ebghtl.rdb (weight 1.24869) # T0361.t2k.str2.rdb (weight 1.54758) # T0361.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 T0361.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0361 # 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 T0361.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 22 # # ============================================ # Comments from T0361.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0361 # 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 T0361.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 22 # # ============================================ # Comments from T0361.t2k.str2.rdb # ============================================ # TARGET T0361 # 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 T0361.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 22 # # ============================================ # Comments from T0361.t2k.alpha.rdb # ============================================ # TARGET T0361 # 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 T0361.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 22 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0602 0.1204 0.8194 2 A 0.1111 0.2335 0.6554 3 T 0.1342 0.2842 0.5816 4 L 0.0885 0.3442 0.5674 5 T 0.1131 0.2831 0.6038 6 E 0.0648 0.5052 0.4300 7 D 0.0722 0.5894 0.3383 8 D 0.0328 0.8189 0.1483 9 V 0.0301 0.8824 0.0875 10 L 0.0295 0.8930 0.0775 11 E 0.0351 0.8593 0.1056 12 Q 0.0262 0.8423 0.1315 13 L 0.0267 0.7759 0.1974 14 D 0.0276 0.5979 0.3745 15 A 0.0297 0.4070 0.5633 16 Q 0.0644 0.2351 0.7005 17 D 0.0480 0.1946 0.7573 18 N 0.0783 0.1307 0.7909 19 L 0.0058 0.9311 0.0631 20 F 0.0048 0.9539 0.0413 21 S 0.0047 0.9576 0.0377 22 F 0.0047 0.9592 0.0361 23 M 0.0047 0.9601 0.0352 24 K 0.0047 0.9601 0.0352 25 T 0.0047 0.9588 0.0365 26 A 0.0047 0.9580 0.0373 27 H 0.0047 0.9596 0.0357 28 S 0.0048 0.9582 0.0370 29 I 0.0048 0.9564 0.0388 30 L 0.0047 0.9552 0.0401 31 L 0.0048 0.9558 0.0395 32 Q 0.0054 0.9448 0.0498 33 G 0.0052 0.9442 0.0506 34 I 0.0052 0.9414 0.0533 35 R 0.0050 0.9397 0.0553 36 Q 0.0052 0.9143 0.0805 37 F 0.0067 0.9026 0.0907 38 L 0.0103 0.8935 0.0962 39 P 0.0069 0.8769 0.1162 40 S 0.0096 0.8360 0.1544 41 L 0.0277 0.7327 0.2396 42 F 0.0919 0.4512 0.4568 43 V 0.0811 0.3714 0.5475 44 D 0.0432 0.3615 0.5954 45 N 0.0626 0.2212 0.7162 46 D 0.0203 0.5557 0.4240 47 E 0.0151 0.8906 0.0943 48 E 0.0288 0.8936 0.0776 49 I 0.0228 0.9152 0.0621 50 V 0.0198 0.9242 0.0560 51 E 0.0228 0.9111 0.0661 52 Y 0.0310 0.8647 0.1044 53 A 0.0518 0.7845 0.1637 54 V 0.0558 0.7316 0.2126 55 K 0.0305 0.7476 0.2219 56 P 0.0291 0.7564 0.2145 57 L 0.0424 0.6533 0.3043 58 L 0.0727 0.5042 0.4231 59 A 0.0555 0.3871 0.5573 60 Q 0.0367 0.2246 0.7387 61 S 0.0480 0.0863 0.8657 62 G 0.0612 0.0524 0.8864 63 P 0.0787 0.1164 0.8050 64 L 0.0703 0.3070 0.6228 65 D 0.0714 0.4318 0.4968 66 D 0.1177 0.5644 0.3179 67 I 0.1533 0.5989 0.2479 68 D 0.1556 0.6628 0.1816 69 V 0.1604 0.7481 0.0915 70 A 0.0717 0.8776 0.0507 71 L 0.0713 0.8779 0.0508 72 R 0.0357 0.9169 0.0473 73 L 0.0407 0.9004 0.0589 74 I 0.0181 0.9224 0.0595 75 Y 0.0141 0.8932 0.0927 76 A 0.0179 0.8395 0.1426 77 L 0.0358 0.6561 0.3081 78 G 0.0390 0.4691 0.4919 79 K 0.0820 0.3681 0.5499 80 M 0.1793 0.2504 0.5703 81 D 0.1098 0.2481 0.6421 82 K 0.0113 0.7907 0.1980 83 W 0.0128 0.7944 0.1927 84 L 0.0123 0.8397 0.1480 85 Y 0.0111 0.9009 0.0880 86 A 0.0080 0.8996 0.0924 87 D 0.0185 0.8985 0.0831 88 I 0.0049 0.9521 0.0430 89 T 0.0047 0.9577 0.0376 90 H 0.0048 0.9543 0.0408 91 F 0.0047 0.9579 0.0374 92 S 0.0047 0.9579 0.0374 93 Q 0.0047 0.9521 0.0431 94 Y 0.0047 0.9521 0.0432 95 W 0.0047 0.9549 0.0404 96 H 0.0049 0.9473 0.0478 97 Y 0.0050 0.9315 0.0636 98 L 0.0090 0.8859 0.1051 99 N 0.0118 0.7611 0.2271 100 E 0.0213 0.5279 0.4508 101 Q 0.0591 0.1614 0.7795 102 D 0.0380 0.1782 0.7838 103 E 0.0517 0.1868 0.7615 104 T 0.1215 0.1928 0.6857 105 P 0.2227 0.1248 0.6525 106 G 0.2075 0.1037 0.6887 107 F 0.2038 0.1122 0.6840 108 A 0.1550 0.1104 0.7346 109 D 0.1286 0.1454 0.7260 110 D 0.0238 0.7389 0.2373 111 I 0.0542 0.7500 0.1958 112 T 0.0705 0.7689 0.1606 113 W 0.0535 0.8104 0.1360 114 D 0.0634 0.7500 0.1866 115 F 0.0248 0.8419 0.1333 116 I 0.0073 0.8962 0.0965 117 S 0.0073 0.8610 0.1317 118 N 0.0086 0.8448 0.1466 119 V 0.0210 0.8292 0.1498 120 N 0.0444 0.8005 0.1552 121 S 0.0598 0.7996 0.1406 122 I 0.0413 0.8421 0.1167 123 T 0.0402 0.7960 0.1638 124 R 0.0354 0.6461 0.3185 125 N 0.0532 0.3503 0.5965 126 A 0.0552 0.2335 0.7112 127 T 0.0598 0.3279 0.6123 128 L 0.0623 0.3359 0.6019 129 Y 0.0570 0.3750 0.5680 130 D 0.0439 0.4815 0.4746 131 A 0.0421 0.5345 0.4233 132 L 0.0624 0.5481 0.3895 133 K 0.0717 0.4696 0.4587 134 A 0.0654 0.3797 0.5548 135 M 0.0497 0.2807 0.6696 136 K 0.0295 0.3074 0.6630 137 F 0.0389 0.3326 0.6285 138 A 0.0238 0.6460 0.3301 139 D 0.0106 0.8130 0.1764 140 F 0.0087 0.9163 0.0750 141 A 0.0076 0.9384 0.0540 142 V 0.0060 0.9442 0.0497 143 W 0.0057 0.9446 0.0497 144 S 0.0054 0.9441 0.0505 145 E 0.0051 0.9433 0.0516 146 A 0.0060 0.9314 0.0626 147 R 0.0069 0.9032 0.0899 148 F 0.0074 0.8809 0.1117 149 S 0.0076 0.8405 0.1519 150 G 0.0077 0.7979 0.1944 151 M 0.0131 0.8502 0.1367 152 V 0.0153 0.8743 0.1105 153 K 0.0086 0.9288 0.0626 154 T 0.0082 0.9481 0.0437 155 A 0.0060 0.9551 0.0390 156 L 0.0069 0.9563 0.0368 157 T 0.0060 0.9553 0.0387 158 L 0.0088 0.9494 0.0418 159 A 0.0062 0.9525 0.0412 160 V 0.0047 0.9566 0.0387 161 T 0.0047 0.9586 0.0367 162 T 0.0048 0.9557 0.0395 163 T 0.0048 0.9532 0.0420 164 L 0.0050 0.9355 0.0595 165 K 0.0058 0.8779 0.1163 166 E 0.0114 0.7418 0.2468 167 L 0.0473 0.4450 0.5078 168 T 0.0486 0.1140 0.8373 169 P 0.0318 0.0563 0.9119