# This file is the result of combining several RDB files, specifically # T0316.t06.dssp-ebghstl.rdb (weight 1.53986) # T0316.t06.stride-ebghtl.rdb (weight 1.24869) # T0316.t06.str2.rdb (weight 1.54758) # T0316.t06.alpha.rdb (weight 0.659012) # T0316.t04.dssp-ebghstl.rdb (weight 1.53986) # T0316.t04.stride-ebghtl.rdb (weight 1.24869) # T0316.t04.str2.rdb (weight 1.54758) # T0316.t04.alpha.rdb (weight 0.659012) # T0316.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0316.t2k.stride-ebghtl.rdb (weight 1.24869) # T0316.t2k.str2.rdb (weight 1.54758) # T0316.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 T0316.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.t06-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 2446 # # ============================================ # Comments from T0316.t06.stride-ebghtl.rdb # ============================================ # TARGET T0316 # Using neural net t06-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 T0316.t06-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 2446 # # ============================================ # Comments from T0316.t06.str2.rdb # ============================================ # TARGET T0316 # 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 T0316.t06-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 2446 # # ============================================ # Comments from T0316.t06.alpha.rdb # ============================================ # TARGET T0316 # Using neural net t06-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 T0316.t06-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 2446 # # ============================================ # Comments from T0316.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 1903 # # ============================================ # Comments from T0316.t04.stride-ebghtl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 1903 # # ============================================ # Comments from T0316.t04.str2.rdb # ============================================ # TARGET T0316 # 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 T0316.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 1903 # # ============================================ # Comments from T0316.t04.alpha.rdb # ============================================ # TARGET T0316 # 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 T0316.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 1903 # # ============================================ # Comments from T0316.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 340 # # ============================================ # Comments from T0316.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 340 # # ============================================ # Comments from T0316.t2k.str2.rdb # ============================================ # TARGET T0316 # 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 T0316.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 340 # # ============================================ # Comments from T0316.t2k.alpha.rdb # ============================================ # TARGET T0316 # 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 T0316.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 340 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1085 0.0519 0.8396 2 S 0.1410 0.0602 0.7987 3 D 0.1230 0.0815 0.7955 4 N 0.0654 0.0721 0.8624 5 S 0.0326 0.1436 0.8239 6 K 0.0563 0.0577 0.8860 7 T 0.1734 0.0166 0.8100 8 R 0.6471 0.0044 0.3485 9 V 0.9209 0.0032 0.0758 10 V 0.9312 0.0032 0.0656 11 V 0.9287 0.0034 0.0679 12 G 0.9082 0.0040 0.0877 13 M 0.7276 0.0214 0.2509 14 S 0.2662 0.0321 0.7017 15 G 0.1237 0.0620 0.8143 16 G 0.0637 0.1756 0.7607 17 V 0.0419 0.5993 0.3588 18 D 0.0155 0.7748 0.2098 19 S 0.0051 0.9155 0.0794 20 S 0.0048 0.9551 0.0402 21 V 0.0047 0.9597 0.0357 22 T 0.0047 0.9599 0.0354 23 A 0.0047 0.9602 0.0351 24 L 0.0047 0.9609 0.0344 25 L 0.0047 0.9605 0.0348 26 L 0.0047 0.9588 0.0365 27 K 0.0048 0.9502 0.0450 28 E 0.0057 0.9037 0.0905 29 Q 0.0402 0.4443 0.5155 30 G 0.0378 0.0340 0.9282 31 Y 0.1105 0.0192 0.8703 32 D 0.5421 0.0167 0.4412 33 V 0.7934 0.0059 0.2006 34 I 0.8304 0.0319 0.1377 35 G 0.9015 0.0080 0.0906 36 I 0.9143 0.0057 0.0800 37 F 0.9042 0.0065 0.0893 38 M 0.8644 0.0121 0.1235 39 K 0.7774 0.0299 0.1927 40 N 0.6425 0.0319 0.3256 41 W 0.4131 0.0547 0.5321 42 D 0.2795 0.0583 0.6622 43 D 0.1509 0.1024 0.7467 44 T 0.0834 0.1060 0.8106 45 D 0.0623 0.1069 0.8308 46 E 0.0602 0.0998 0.8400 47 N 0.0880 0.1056 0.8063 48 G 0.1148 0.0907 0.7944 49 V 0.2082 0.0973 0.6945 50 C 0.2552 0.0784 0.6664 51 T 0.1483 0.1009 0.7508 52 A 0.0723 0.2668 0.6609 53 T 0.0164 0.7215 0.2621 54 E 0.0166 0.6880 0.2954 55 D 0.0221 0.7020 0.2759 56 Y 0.0052 0.9353 0.0595 57 K 0.0049 0.9482 0.0469 58 D 0.0048 0.9543 0.0409 59 V 0.0047 0.9590 0.0363 60 V 0.0047 0.9605 0.0349 61 A 0.0047 0.9604 0.0349 62 V 0.0047 0.9596 0.0357 63 A 0.0047 0.9579 0.0374 64 D 0.0053 0.9457 0.0491 65 Q 0.0068 0.9070 0.0862 66 I 0.0468 0.4682 0.4849 67 G 0.0507 0.0142 0.9352 68 I 0.0717 0.0082 0.9201 69 P 0.1847 0.0121 0.8032 70 Y 0.6404 0.0082 0.3513 71 Y 0.8554 0.0063 0.1383 72 S 0.9106 0.0047 0.0847 73 V 0.8613 0.0099 0.1288 74 N 0.6166 0.0100 0.3734 75 F 0.0305 0.6115 0.3580 76 E 0.0102 0.7387 0.2511 77 K 0.0076 0.8823 0.1100 78 E 0.0082 0.8975 0.0943 79 Y 0.0112 0.8710 0.1177 80 W 0.0069 0.8999 0.0932 81 D 0.0076 0.8955 0.0969 82 R 0.0091 0.8405 0.1504 83 V 0.0167 0.8283 0.1550 84 F 0.0087 0.8834 0.1079 85 E 0.0066 0.9286 0.0648 86 Y 0.0049 0.9375 0.0577 87 F 0.0048 0.9427 0.0525 88 L 0.0048 0.9478 0.0474 89 A 0.0049 0.9507 0.0443 90 E 0.0058 0.9428 0.0514 91 Y 0.0094 0.9189 0.0717 92 R 0.0094 0.8623 0.1282 93 A 0.0351 0.5184 0.4465 94 G 0.0311 0.1327 0.8362 95 R 0.0737 0.0471 0.8792 96 T 0.0942 0.0273 0.8785 97 P 0.0659 0.0438 0.8903 98 N 0.0876 0.0371 0.8753 99 P 0.1207 0.1109 0.7684 100 D 0.2471 0.1455 0.6074 101 V 0.2364 0.3065 0.4570 102 M 0.1846 0.3009 0.5144 103 C 0.0876 0.3176 0.5948 104 N 0.0763 0.2556 0.6681 105 K 0.0611 0.4814 0.4575 106 E 0.1575 0.5104 0.3321 107 I 0.3062 0.4107 0.2831 108 K 0.2730 0.3812 0.3458 109 F 0.0301 0.8085 0.1614 110 K 0.0074 0.9245 0.0681 111 A 0.0057 0.9425 0.0518 112 F 0.0052 0.9494 0.0454 113 L 0.0055 0.9544 0.0400 114 D 0.0052 0.9528 0.0420 115 Y 0.0050 0.9513 0.0436 116 A 0.0051 0.9494 0.0455 117 I 0.0052 0.9406 0.0542 118 T 0.0061 0.8715 0.1224 119 L 0.0441 0.3891 0.5668 120 G 0.0476 0.0190 0.9333 121 A 0.0923 0.0090 0.8987 122 D 0.2309 0.0463 0.7228 123 Y 0.8990 0.0089 0.0921 124 V 0.9190 0.0056 0.0754 125 A 0.8955 0.0071 0.0974 126 T 0.7505 0.0195 0.2300 127 G 0.2837 0.0330 0.6833 128 H 0.2705 0.0918 0.6377 129 Y 0.5165 0.1124 0.3711 130 A 0.7053 0.0704 0.2243 131 R 0.7526 0.0529 0.1945 132 V 0.7828 0.0377 0.1795 133 A 0.7193 0.0337 0.2470 134 R 0.6528 0.0397 0.3075 135 D 0.2502 0.0725 0.6773 136 E 0.0670 0.1120 0.8209 137 D 0.0642 0.0619 0.8740 138 G 0.1274 0.0487 0.8239 139 T 0.4959 0.0231 0.4810 140 V 0.8235 0.0107 0.1658 141 H 0.8619 0.0152 0.1229 142 M 0.8788 0.0144 0.1069 143 L 0.8209 0.0312 0.1479 144 R 0.7784 0.0294 0.1921 145 G 0.6318 0.0438 0.3244 146 V 0.4278 0.0556 0.5166 147 D 0.2428 0.0519 0.7053 148 N 0.0380 0.2895 0.6724 149 G 0.0483 0.2460 0.7057 150 K 0.0843 0.2501 0.6656 151 D 0.1787 0.1581 0.6631 152 Q 0.3379 0.2164 0.4457 153 T 0.4675 0.2500 0.2824 154 Y 0.4450 0.3398 0.2152 155 F 0.4110 0.3610 0.2280 156 L 0.2992 0.3727 0.3281 157 S 0.1937 0.2971 0.5092 158 Q 0.1539 0.1992 0.6469 159 L 0.1549 0.0461 0.7990 160 S 0.0970 0.0393 0.8637 161 Q 0.0062 0.8785 0.1154 162 E 0.0059 0.8927 0.1015 163 Q 0.0070 0.8921 0.1008 164 L 0.0095 0.8907 0.0998 165 Q 0.0103 0.8447 0.1450 166 K 0.0139 0.7454 0.2407 167 T 0.0379 0.6263 0.3359 168 M 0.0985 0.3869 0.5146 169 F 0.1117 0.1745 0.7138 170 P 0.0909 0.1853 0.7237 171 L 0.0389 0.4562 0.5049 172 G 0.0355 0.4106 0.5539 173 H 0.0377 0.4272 0.5352 174 L 0.0772 0.1951 0.7277 175 E 0.0717 0.1435 0.7847 176 K 0.0293 0.6199 0.3508 177 P 0.0062 0.9296 0.0642 178 E 0.0052 0.9492 0.0456 179 V 0.0048 0.9569 0.0383 180 R 0.0047 0.9587 0.0365 181 R 0.0048 0.9605 0.0348 182 L 0.0047 0.9605 0.0348 183 A 0.0047 0.9591 0.0361 184 E 0.0050 0.9513 0.0437 185 E 0.0055 0.9206 0.0740 186 A 0.0425 0.3989 0.5586 187 G 0.0351 0.0253 0.9396 188 L 0.0689 0.0191 0.9119 189 S 0.2187 0.0495 0.7318 190 T 0.2641 0.1624 0.5735 191 A 0.2527 0.1581 0.5892 192 K 0.1934 0.0750 0.7317 193 K 0.1563 0.0582 0.7855 194 K 0.1033 0.2327 0.6640 195 D 0.1148 0.1877 0.6976 196 S 0.1916 0.1479 0.6605 197 T 0.1785 0.0798 0.7418 198 G 0.1963 0.0655 0.7382 199 I 0.5025 0.0511 0.4464 200 C 0.5508 0.0585 0.3908 201 F 0.5972 0.0521 0.3507 202 I 0.4299 0.0477 0.5224 203 G 0.2082 0.0475 0.7444 204 E 0.0954 0.0822 0.8223 205 K 0.0378 0.0414 0.9208