3 function // 0=FindLUCA,1=FindScores,2=FindNonStartAAs,3=FindNonGlobAAs,4=GlobOptimizeGroups, 5=TestData 0 FIRST_AA_IS_TESTED // 1=all AAs are tested at the 1st position, 0=>see the next row M firstAA // only when FIRST_AA_IS_TESTED = 0 ----------------------------------------------------------- 0 input database // 0=Leipzig, 1=UCSC, 2=Poznan, 3=testLeipzig, 4=testUCSC 1 ARCHAEA_ARE_INCLUDED 1 BACTERIA_ARE_INCLUDED 1 EUKARYOTES_ARE_INCLUDED 0 VIRUSES_ARE_INCLUDED // only for database = 0 0 ONLY_PARTICULAR_SPECIES_ARE_SELECTED 0 BACTERIAL_&_EUKARYOTIC_WEIGHTS_ARE_EQUAL // only for function = 0 16 min number of assignments 10 max number of non-starting AAs ----------------------------------------------------------- D acidType // R means tRNAs, D means tRNA genes (=tDNAs) 0 MODIFIED_NUCLEOTIDES // 1=are distinguished (only for tRNAs), 0=not, 2=combined 0 topology // 0 = periodic code 1 X_IS_INCLUDED // Ini 1 O_IS_INCLUDED // Sup 1 Z_IS_INCLUDED // Sec, i.e., selenocisteine 1 MX_MOVE_TOGETHER // 1=Met and fMet/Met-ini move together, 0=no 1 NONSTANDARD_ASSIGNMENTS // are 0=ignored or 1=processed according to amino acids 0 ISOACCEPTORS //1=similarities among isoacceptor tRNAs/tDNAs are also computed, 0=no 0 isoWeight // vs. alloacceptorWeight=1 // only when ISOACCEPTORS = 1 ----------------------------------------------------------- 5 numOfOptimizableGroups 1 groupWeight // vs. familyWeight=1 ----------------------------------------------------------- 2 numOfStableAAs G P stableAAs ----------------------------------------------------------- 0 numOfNonStartAAs nonStartAAs ----------------------------------------------------------- 1 ADAPTATION TO A GLOBAL STRUCTURE // 1 = yes, 0 = no 3 globStart // numbering starts from 1 ----------------------------------------------------------- 0 numOfNonGlobAAs nonGlobAAs ----------------------------------------------------------- 0 included_parts // 0=Giege,1=E.coli,2=S.cerevisiae,3=blocks,4=custom 0 IE cutoff min // only when included_parts < 3 =0(all), =1(identity elements (IEs)), =3(effective IEs), =5(major IEs), =10(most MIEs) 0 aaRS_class // 0 = both, 1 = type I, 2 = type II ----------------if-database=1-&-function!=1---------------- 67 score cutoff min 150 score cutoff max 0 isoscore cutoff min 150 isoscore cutoff max 0 isoscore_ac cutoff min 150 isoscore_ac cutoff max ----------------------------------------------------------- 1 numOfGenAlgorithmRuns 2 NumOfMatingsAndMutations 16 numOfTrimmedClassifications 2 4 8 16 32 48 64 0 softwareBruteForce // 0 = basic level, 1,2 = more brute force 0 hardwareBruteForce // 0 = basic level, 1,2 = more brute force ----------------------------------------------------------- 1 SAVE_DATA // save x_tRNA.txt or x_tDNA.txt on a harddisk 0 PRINT_UNRECOMMENDED_DETAILS // if function < 4, the ouput files can get too long -----------------if-DOMAINS_ARE_WEIGHTED=1----------------- 1 archaealWeight 1 bacterialWeight 1 eukaryoticWeight 0 virusesWeight -----------------------if-function=0----------------------- 1 domainStep[0] // archaeal weight 1 domainStart[0] 3 domainStop[0] 1 domainStep[0] // bacterial weight 1 domainStart[0] 3 domainStop[0] 1 domainStep[0] // eukaryotic weight 1 domainStart[0] 3 domainStop[0] 1 domainStep[0] // viral weight 0 domainStart[0] 0 domainStop[0] ----------------------if-database=1------------------------ 1 ISOTYPE_MUST_BE_BEST_MODEL 0 primary ----------------if-database=1-&-function=1----------------- 0.5 scoreStep[0] // min score 65 scoreStart[0] 110 scoreStop[0] 1 scoreStep[1] // min isoscore 0 scoreStart[1] 0 scoreStop[1] 1 scoreStep[2] // min isoscore_ac 0 scoreStart[2] 0 scoreStop[2] 1 scoreStep[3] // max score 150 scoreStart[3] 150 scoreStop[3] 1 scoreStep[4] // max isoscore 150 scoreStart[4] 150 scoreStop[4] 1 scoreStep[5] // max isoscore_ac 150 scoreStart[5] 150 scoreStop[5] ---------------------included_parts=3---------------------- 1 IS_ACCEPTOR_STEM 3 IECutOffMin3[0] 1 IS_D-ARM 3 IECutOffMin3[1] 1 IS_ANTICODON_ARM 3 IECutOffMin3[2] 1 IS_VARIABLE_LOOP 3 IECutOffMin3[3] 1 IS_T-ARM 3 IECutOffMin3[4] 1 IS_8th_SITE 3 IECutOffMin3[5] 1 IS_9th_SITE 3 IECutOffMin3[6] 1 IS_26th_SITE 3 IECutOffMin3[7] 1 IS_73rd_SITE 3 IECutOffMin3[8] 1 IS_74th_SITE 3 IECutOffMin3[9] 1 IS_75th_SITE 3 IECutOffMin3[10] 1 IS_76th_SITE 3 IECutOffMin3[11] 1 IS_ANTICODON 1 IS_INTERSECTION_WITH_GIEGE 0 IS_INTERSECTION_WITH_E.COLI 0 IS_INTERSECTION_WITH_S.CEREVISIAE ---------------------included_parts=4---------------------- 11111111 Acceptor stem 5'->3' // 1 = included, 0 = excluded 11111111111 3'->5' 11111111111111111 D-arm 5'->3' 1111 3'->5' 1111111111111 Anticodon arm 5'->3' 111111 3'->5' 11111111111111 Variable loop 5'->3' 1111111111 3'->5' 111111111111 T-arm 5'->3' 11111 3'->5' ------------------------in-reality------------------------- Included sites of tDNAs (written only after the start of the program): Acceptor stem: 11111111 D-arm:11111111111111111 11111111111 1111 Anticodon arm:1111111111111 Variable loop:11111111111111 T-arm:111111111111 11111 1111111111 11111 -----------------------------------------------------------