# This file is the result of combining several RDB files, specifically # YGR035W-A.t2k.dssp-ebghstl.rdb (weight 1.53986) # YGR035W-A.t2k.stride-ebghtl.rdb (weight 1.24869) # YGR035W-A.t2k.str2.rdb (weight 1.54758) # YGR035W-A.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 YGR035W-A.t2k.dssp-ebghstl.rdb # ============================================ # TARGET YGR035W-A # 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 YGR035W-A.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 1 # # ============================================ # Comments from YGR035W-A.t2k.stride-ebghtl.rdb # ============================================ # TARGET YGR035W-A # 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 YGR035W-A.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 1 # # ============================================ # Comments from YGR035W-A.t2k.str2.rdb # ============================================ # TARGET YGR035W-A # 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 YGR035W-A.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 1 # # ============================================ # Comments from YGR035W-A.t2k.alpha.rdb # ============================================ # TARGET YGR035W-A # 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 YGR035W-A.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0357 0.2919 0.6724 2 L 0.0717 0.7169 0.2114 3 L 0.0558 0.8139 0.1302 4 Y 0.0526 0.8641 0.0833 5 L 0.0640 0.8594 0.0765 6 Y 0.0789 0.8562 0.0649 7 I 0.0971 0.8405 0.0624 8 L 0.0962 0.8371 0.0667 9 Y 0.0883 0.8291 0.0825 10 I 0.0782 0.8164 0.1053 11 A 0.0664 0.7989 0.1347 12 L 0.0597 0.7618 0.1785 13 K 0.0769 0.6580 0.2651 14 T 0.1154 0.5380 0.3466 15 V 0.1561 0.5041 0.3398 16 S 0.1600 0.4905 0.3495 17 H 0.2243 0.4454 0.3303 18 L 0.3649 0.3540 0.2810 19 F 0.4728 0.2485 0.2787 20 F 0.4472 0.1742 0.3786 21 C 0.2827 0.1242 0.5931 22 N 0.1403 0.1342 0.7255 23 P 0.0736 0.3534 0.5730 24 C 0.1018 0.3724 0.5258 25 F 0.1362 0.3909 0.4729 26 R 0.1214 0.3421 0.5365 27 N 0.1440 0.2570 0.5990 28 L 0.1968 0.1808 0.6224 29 S 0.2174 0.1497 0.6329 30 V 0.1236 0.3534 0.5229 31 G 0.0812 0.3736 0.5452 32 D 0.0844 0.4020 0.5136 33 M 0.1321 0.3544 0.5135 34 L 0.1436 0.2792 0.5772 35 N 0.1153 0.1600 0.7247 36 P 0.0641 0.3998 0.5362 37 R 0.1201 0.3915 0.4885 38 L 0.2229 0.3718 0.4054 39 S 0.2835 0.3223 0.3942 40 L 0.2412 0.4635 0.2954 41 S 0.2699 0.4568 0.2733 42 F 0.2867 0.4151 0.2982 43 F 0.3218 0.3384 0.3398 44 T 0.2335 0.3508 0.4157 45 N 0.1527 0.3098 0.5375 46 H 0.2324 0.2604 0.5071 47 L 0.3642 0.1734 0.4623 48 L 0.3561 0.1112 0.5327 49 C 0.1861 0.0590 0.7549 50 P 0.0769 0.1546 0.7686 51 E 0.0784 0.1279 0.7937 52 A 0.1491 0.0718 0.7791 53 P 0.2510 0.0601 0.6889 54 L 0.6238 0.0577 0.3185 55 I 0.7583 0.0527 0.1890 56 I 0.7403 0.0512 0.2085 57 R 0.5534 0.0605 0.3861 58 G 0.2730 0.0656 0.6614 59 K 0.1374 0.0900 0.7726 60 G 0.1591 0.0948 0.7461 61 S 0.2305 0.1390 0.6305 62 Y 0.2715 0.2421 0.4865 63 S 0.2491 0.3275 0.4234 64 A 0.2198 0.3973 0.3829 65 V 0.1894 0.4128 0.3978 66 G 0.1613 0.3623 0.4764 67 N 0.1827 0.3792 0.4381 68 F 0.2550 0.3745 0.3705 69 F 0.2811 0.3306 0.3883 70 S 0.2238 0.2721 0.5042 71 R 0.1496 0.2211 0.6293 72 K 0.0887 0.1260 0.7854 73 K 0.0392 0.0442 0.9166