Wise2 - database searching mode Program: genewisedb version: $Name: wise2-2-0 $ released: unreleased This program is freely distributed under a Gnu Public License. See -version for more info on copyright Bugs and credits to Ewan Birney ----------------------------------------------------- Algorithm type: GeneWise Search algorithm used: 623 Implementation: Single Threaded processor (serial) Search mode: Single genomic vs protein db Protein info from: rrm.HMM Dna info from: short.dna Start/End (protein) default Gene Paras: human.gf Codon Table: codon.table Subs error: 1e-05 Indel error: 1e-05 Model splice? model Model codon bias? flat Model intron bias? tied Null model syn Alignment Alg 623L # #WARNING! # # Your alignment algorithm is different from your search algorithm. # This is probably quite sensible but will lead to differing scores. # Use the search score as an indicator of the significance of the match # Read the docs for more information # #High Score list #Protein ID DNA Str ID Bits Evalue -------------------------------------------------------------------------- Protein SEED DNA [+] HSHNCPA1 100.94 #Alignments ----------------------------------------------------------------------- >Results for SEED vs HSHNCPA1 (forward) [0] genewisedb output Score 92.71 bits over entire alignment. This will be different from per-alignment scores. See manual for details For computer parsable output, try genewisedb -help or read the manual Scores as bits over a synchronous coding model Alignment 1 Score 92.71 (Bits) SEED 1 LFVGNLPPDVTEEDLKDLFSKFGPIVSIKIVRDIIEKPKETGKSKGFAF FVG++ +D+ E+ L+D+F+++G+I+ I+I++D + GK +GFA+ IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD-----RGSGKKRGFAx HSHNCPA1 17 atgggaaggaggcccagttgctgaaggagaaag cgagaaagtgt tttggtaaacaaaatgaataaagatattattca ggggaaggtct atttctaactaatcaatttagtaatagtacgtc actcgagctcN SEED 50 VEFESEEDAEKALEALNGKELGGRKLRV V+F+++++++K + ++++G++++V VTFDDHDSVDKIVI-QKYHTVNGHNCEV HSHNCPA1 149 gatggcgtggaaga catcagagcatgg tctaaaactaattt aaaactagaagat actcctccgtgtct gacttgtccctat // 0.00 [-1:-1 "LOOP_STATE" 0],[0:15 "RANDOM_SEQUENCE" 0] -5.85 [-1:0 "MATCH_STATE" -2026],[15:18 "CODON" -2026] 3.21 [0:1 "MATCH_STATE" 1114],[18:21 "CODON" 1114] 3.13 [1:2 "MATCH_STATE" 1086],[21:24 "CODON" 1086] 2.46 [2:3 "MATCH_STATE" 853],[24:27 "CODON" 853] 1.79 [3:4 "MATCH_STATE" 621],[27:30 "CODON" 621] 0.64 [4:5 "MATCH_STATE" 223],[30:33 "CODON" 223] -0.58 [5:6 "MATCH_STATE" -202],[33:36 "CODON" -202] 0.63 [6:7 "MATCH_STATE" 218],[36:39 "CODON" 218] 2.41 [7:8 "MATCH_STATE" 834],[39:42 "CODON" 834] 1.73 [8:9 "MATCH_STATE" 600],[42:45 "CODON" 600] -1.19 [9:10 "MATCH_STATE" -414],[45:48 "CODON" -414] 2.48 [10:11 "MATCH_STATE" 859],[48:51 "CODON" 859] 0.49 [11:12 "MATCH_STATE" 171],[51:54 "CODON" 171] -0.94 [12:13 "MATCH_STATE" -326],[54:57 "CODON" -326] 2.82 [13:14 "MATCH_STATE" 978],[57:60 "CODON" 978] 1.79 [14:15 "MATCH_STATE" 622],[60:63 "CODON" 622] 2.12 [15:16 "MATCH_STATE" 736],[63:66 "CODON" 736] 1.19 [16:17 "MATCH_STATE" 413],[66:69 "CODON" 413] 4.21 [17:18 "MATCH_STATE" 1458],[69:72 "CODON" 1458] 0.97 [18:19 "MATCH_STATE" 335],[72:75 "CODON" 335] 1.71 [19:20 "MATCH_STATE" 591],[75:78 "CODON" 591] 2.81 [20:21 "MATCH_STATE" 975],[78:81 "CODON" 975] 3.51 [21:22 "MATCH_STATE" 1215],[81:84 "CODON" 1215] 1.33 [22:23 "MATCH_STATE" 460],[84:87 "CODON" 460] 2.71 [23:24 "MATCH_STATE" 940],[87:90 "CODON" 940] 1.19 [24:25 "MATCH_STATE" 413],[90:93 "CODON" 413] -2.42 [25:26 "MATCH_STATE" -838],[93:96 "CODON" -838] 2.22 [26:27 "MATCH_STATE" 768],[96:99 "CODON" 768] 0.51 [27:28 "MATCH_STATE" 176],[99:102 "CODON" 176] 2.16 [28:29 "MATCH_STATE" 749],[102:105 "CODON" 749] 1.94 [29:30 "MATCH_STATE" 672],[105:108 "CODON" 672] 0.77 [30:31 "MATCH_STATE" 268],[108:111 "CODON" 268] 2.97 [31:32 "MATCH_STATE" 1028],[111:114 "CODON" 1028] -0.05 [32:33 "DELETE_STATE" -18],[114:114 "INSERT" -18] -0.07 [33:34 "DELETE_STATE" -24],[114:114 "INSERT" -24] -0.05 [34:35 "DELETE_STATE" -18],[114:114 "INSERT" -18] -0.05 [35:36 "DELETE_STATE" -18],[114:114 "INSERT" -18] -0.05 [36:37 "DELETE_STATE" -19],[114:114 "INSERT" -19] 0.68 [37:38 "MATCH_STATE" 234],[114:117 "CODON" 234] -0.64 [38:39 "MATCH_STATE" -221],[117:120 "CODON" -221] -0.05 [39:40 "MATCH_STATE" -18],[120:123 "CODON" -18] 2.51 [40:41 "MATCH_STATE" 870],[123:126 "CODON" 870] 1.94 [41:42 "MATCH_STATE" 673],[126:129 "CODON" 673] -0.47 [42:43 "MATCH_STATE" -162],[129:132 "CODON" -162] 2.27 [43:44 "MATCH_STATE" 788],[132:135 "CODON" 788] 3.24 [44:45 "MATCH_STATE" 1122],[135:138 "CODON" 1122] 3.06 [45:46 "MATCH_STATE" 1062],[138:141 "CODON" 1062] 2.52 [46:47 "MATCH_STATE" 872],[141:144 "CODON" 872] 3.24 [47:48 "MATCH_STATE" 1122],[144:147 "CODON" 1122] 3.30 [48:49 "MATCH_STATE" 1144],[147:150 "CODON" 1144] 1.31 [49:50 "MATCH_STATE" 455],[150:153 "CODON" 455] 4.00 [50:51 "MATCH_STATE" 1386],[153:156 "CODON" 1386] 1.16 [51:52 "MATCH_STATE" 401],[156:159 "CODON" 401] 1.92 [52:53 "MATCH_STATE" 665],[159:162 "CODON" 665] 1.50 [53:54 "MATCH_STATE" 519],[162:165 "CODON" 519] 1.62 [54:55 "MATCH_STATE" 561],[165:168 "CODON" 561] 1.28 [55:56 "MATCH_STATE" 443],[168:171 "CODON" 443] 0.02 [56:57 "MATCH_STATE" 6],[171:174 "CODON" 6] 1.00 [57:58 "MATCH_STATE" 346],[174:177 "CODON" 346] 2.33 [58:59 "MATCH_STATE" 807],[177:180 "CODON" 807] -0.14 [59:60 "MATCH_STATE" -48],[180:183 "CODON" -48] 1.59 [60:61 "MATCH_STATE" 551],[183:186 "CODON" 551] -0.79 [61:62 "MATCH_STATE" -275],[186:189 "CODON" -275] -2.39 [62:63 "DELETE_STATE" -827],[189:189 "INSERT" -827] -0.46 [63:64 "MATCH_STATE" -160],[189:192 "CODON" -160] -0.36 [64:65 "MATCH_STATE" -125],[192:195 "CODON" -125] -0.62 [65:66 "MATCH_STATE" -216],[195:198 "CODON" -216] 0.96 [66:67 "MATCH_STATE" 333],[198:201 "CODON" 333] 0.72 [67:68 "MATCH_STATE" 248],[201:204 "CODON" 248] 1.26 [68:69 "MATCH_STATE" 438],[204:207 "CODON" 438] 1.71 [69:70 "MATCH_STATE" 591],[207:210 "CODON" 591] 2.74 [70:71 "MATCH_STATE" 951],[210:213 "CODON" 951] 1.91 [71:72 "MATCH_STATE" 661],[213:216 "CODON" 661] 0.21 [72:73 "MATCH_STATE" 74],[216:219 "CODON" 74] 0.91 [73:74 "MATCH_STATE" 314],[219:222 "CODON" 314] 0.34 [74:75 "MATCH_STATE" 119],[222:225 "CODON" 119] 2.75 [75:76 "MATCH_STATE" 954],[225:228 "CODON" 954] 0.00 [76:0 "LOOP_STATE" 0],[228:413 "RANDOM_SEQUENCE" 0] 0.00 [0:0 "END" 0],[413:414 "END" 0] //