# This file is the result of combining several RDB files, specifically # T0215.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0215.t2k.stride-ebghtl.rdb (weight 1.24869) # T0215.t2k.str2.rdb (weight 1.54758) # T0215.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 T0215.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0215 # 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 T0215.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 3 # # ============================================ # Comments from T0215.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0215 # 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 T0215.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 3 # # ============================================ # Comments from T0215.t2k.str2.rdb # ============================================ # TARGET T0215 # 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 T0215.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 3 # # ============================================ # Comments from T0215.t2k.alpha.rdb # ============================================ # TARGET T0215 # 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 T0215.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 3 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0860 0.0651 0.8488 2 G 0.1587 0.0835 0.7578 3 T 0.1652 0.0994 0.7354 4 S 0.1698 0.1625 0.6677 5 H 0.1907 0.1951 0.6141 6 H 0.2045 0.1973 0.5982 7 H 0.2162 0.1860 0.5978 8 H 0.2044 0.1748 0.6208 9 H 0.1757 0.1567 0.6677 10 H 0.1375 0.1368 0.7256 11 S 0.1051 0.1490 0.7460 12 S 0.0956 0.1465 0.7579 13 G 0.1000 0.1297 0.7703 14 R 0.1961 0.1685 0.6353 15 E 0.2941 0.2348 0.4710 16 N 0.3274 0.2369 0.4356 17 L 0.4173 0.2418 0.3409 18 Y 0.4954 0.2240 0.2806 19 F 0.4878 0.2533 0.2589 20 Q 0.3339 0.2924 0.3738 21 G 0.2142 0.3050 0.4808 22 H 0.1716 0.3447 0.4836 23 M 0.1378 0.4019 0.4603 24 R 0.0686 0.3050 0.6264 25 N 0.0665 0.1762 0.7573 26 L 0.0747 0.3584 0.5669 27 S 0.0776 0.4535 0.4689 28 D 0.0789 0.5068 0.4143 29 R 0.0459 0.6713 0.2827 30 A 0.0605 0.6792 0.2603 31 K 0.0658 0.6739 0.2602 32 F 0.0516 0.7838 0.1646 33 E 0.0378 0.8105 0.1517 34 S 0.0447 0.7670 0.1884 35 M 0.0583 0.7122 0.2295 36 I 0.1057 0.4100 0.4843 37 N 0.0685 0.1074 0.8240 38 S 0.0769 0.0784 0.8447 39 P 0.0487 0.2284 0.7229 40 S 0.0829 0.2246 0.6926 41 K 0.0619 0.4933 0.4448 42 S 0.1116 0.5680 0.3203 43 V 0.1722 0.5646 0.2632 44 F 0.2476 0.5065 0.2459 45 V 0.2030 0.4789 0.3180 46 R 0.1394 0.4132 0.4473 47 N 0.1311 0.2906 0.5783 48 L 0.0134 0.7732 0.2134 49 N 0.0080 0.8756 0.1165 50 E 0.0052 0.9321 0.0627 51 L 0.0048 0.9494 0.0458 52 E 0.0050 0.9489 0.0461 53 A 0.0051 0.9502 0.0447 54 L 0.0049 0.9501 0.0449 55 A 0.0051 0.9429 0.0520 56 V 0.0072 0.9110 0.0818 57 R 0.0121 0.8279 0.1599 58 L 0.0336 0.5232 0.4432 59 G 0.0296 0.1830 0.7875 60 K 0.0323 0.2890 0.6787 61 S 0.0592 0.4086 0.5322 62 Y 0.0857 0.6141 0.3002 63 R 0.0987 0.7548 0.1466 64 I 0.0960 0.7480 0.1560 65 Q 0.0545 0.7776 0.1679 66 L 0.0188 0.8710 0.1102 67 D 0.0180 0.8645 0.1176 68 Q 0.0166 0.8435 0.1399 69 A 0.0398 0.7597 0.2005 70 K 0.0541 0.7109 0.2350 71 E 0.0723 0.6667 0.2610 72 K 0.1234 0.5519 0.3247 73 W 0.2029 0.3067 0.4904 74 K 0.2257 0.2161 0.5582 75 V 0.1313 0.1165 0.7522 76 K 0.0442 0.0374 0.9184