# This file is the result of combining several RDB files, specifically # T0262.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0262.t2k.stride-ebghtl.rdb (weight 1.24869) # T0262.t2k.str2.rdb (weight 1.54758) # T0262.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 T0262.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0262 # 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 T0262.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 33 # # ============================================ # Comments from T0262.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0262 # 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 T0262.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 33 # # ============================================ # Comments from T0262.t2k.str2.rdb # ============================================ # TARGET T0262 # 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 T0262.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 33 # # ============================================ # Comments from T0262.t2k.alpha.rdb # ============================================ # TARGET T0262 # 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 T0262.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 33 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 H 0.1145 0.0941 0.7914 2 L 0.1596 0.0790 0.7613 3 T 0.1342 0.0542 0.8117 4 S 0.0806 0.1902 0.7292 5 S 0.0966 0.1449 0.7585 6 L 0.0065 0.9143 0.0793 7 E 0.0056 0.9356 0.0587 8 D 0.0056 0.9359 0.0585 9 A 0.0094 0.9345 0.0561 10 V 0.0151 0.9132 0.0717 11 S 0.0224 0.8684 0.1092 12 T 0.0566 0.7129 0.2305 13 G 0.1299 0.4263 0.4439 14 R 0.1991 0.2875 0.5134 15 R 0.2374 0.2191 0.5436 16 H 0.2036 0.1236 0.6728 17 G 0.1002 0.0736 0.8262 18 N 0.0598 0.0588 0.8814 19 L 0.1057 0.0141 0.8801 20 V 0.2473 0.0071 0.7456 21 A 0.7975 0.0053 0.1972 22 V 0.9202 0.0034 0.0764 23 L 0.9198 0.0043 0.0759 24 L 0.9192 0.0040 0.0768 25 V 0.8259 0.0131 0.1610 26 D 0.5797 0.0147 0.4056 27 V 0.0250 0.7397 0.2353 28 E 0.0089 0.8655 0.1256 29 C 0.0080 0.9156 0.0764 30 L 0.0096 0.9209 0.0695 31 R 0.0132 0.9061 0.0807 32 R 0.0145 0.8230 0.1625 33 R 0.0479 0.2552 0.6968 34 G 0.0421 0.0221 0.9358 35 L 0.1304 0.0111 0.8585 36 K 0.6376 0.0090 0.3535 37 V 0.8672 0.0062 0.1266 38 E 0.8905 0.0063 0.1033 39 R 0.8737 0.0057 0.1206 40 M 0.6181 0.0298 0.3520 41 S 0.1125 0.0667 0.8207 42 K 0.0419 0.0543 0.9038 43 T 0.2480 0.0296 0.7224 44 V 0.8693 0.0044 0.1263 45 Y 0.9198 0.0033 0.0769 46 T 0.8870 0.0060 0.1070 47 V 0.7102 0.0249 0.2650 48 D 0.4752 0.0602 0.4646 49 W 0.2973 0.0650 0.6378 50 V 0.2233 0.0184 0.7582 51 P 0.1161 0.0212 0.8627 52 P 0.0190 0.6974 0.2835 53 E 0.0236 0.7516 0.2248 54 C 0.0483 0.7883 0.1634 55 I 0.1575 0.6547 0.1878 56 A 0.2478 0.5806 0.1717 57 E 0.3130 0.4982 0.1888 58 V 0.3525 0.3975 0.2500 59 R 0.3336 0.2792 0.3873 60 R 0.2369 0.3502 0.4129 61 E 0.1319 0.3668 0.5013 62 S 0.1328 0.3632 0.5040 63 L 0.0876 0.2601 0.6523 64 G 0.0795 0.1652 0.7553 65 R 0.1221 0.1415 0.7364 66 S 0.1299 0.1284 0.7417 67 L 0.0322 0.0618 0.9060