0 input database // 0=Leipzig, 1=UCSC, 2=Poznan, 3=testLeipzig, 4=testUCSC
D acidType // R means tRNAs, D means tRNA genes (=tDNAs)
1 ARCHAEA_ARE_INCLUDED // 1 = yes, 0 = no
1 BACTERIA_ARE_INCLUDED
1 EUKARYOTES_ARE_INCLUDED
0 VIRUSES_ARE_INCLUDED // only for tRNA genes of database 0
0 SPECIES_ARE_SELECTED
0 numOfSpecies
species
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4 function // 0=FindLUCA,1=FindScores,2=FindNonStartAAs,3=FindNonGlobAAs,4=GlobOptimizeGroups,5=TestData
1 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
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0 modified_nucleotides // 1=are distinguished (only for tRNAs), 0=not, 2=combined
0 topology // 0 = periodic code
0 aaRS_class // 0 = amino acids of both classes are included, 1 = type I, 2 = type II
1 X_IS_INCLUDED // Ini, i.e., initiation signals
1 O_IS_INCLUDED // Sup, i.e., termination signals
1 U_IS_INCLUDED // Sec, i.e., selenocisteine
0 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
-----------------------------------------------------------
8 numOfOptimizableGroups
2 numOfOneElementGroups
G P oneElementGroups
1 groupWeight // vs. familyWeight=1
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0 numOfNonStartAAs
nonStartAAs
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1 GLOBAL_ADAPTATION
0 numOfNonGlobAAs
nonGlobAAs
3 globStart // numbering starts from 1
----------------------if-database=1------------------------
1 ISOTYPE_MUST_BE_BEST_MODEL
0 primary
----------------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
----------------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]
-----------------------------------------------------------
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
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0 ISOACCEPTORS //1=similarities among isoacceptor tRNAs/tDNAs are also computed, 0=no
0 isoWeight // vs. alloacceptorWeight=1 // only when ISOACCEPTORS = 1
16 min number of assignments
15 max number of non-starting AAs
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 // default=1
1 bacterialWeight // default=1
1 eukaryoticWeight // default=1
0 virusesWeight // default=0, when some is not default or function=0, then DOMAINS_ARE_WEIGHTED=1
0 BACTERIAL_AND_EUKARYOTIC_WEIGHTS_STAY_EQUAL // only for function = 0
-----------------------if-function=0-----------------------
1 domainStep[0] // archaeal weight
1 domainStart[0]
3 domainStop[0]
1 domainStep[1] // bacterial weight
1 domainStart[1]
3 domainStop[1]
1 domainStep[2] // eukaryotic weight
1 domainStart[2]
3 domainStop[2]
1 domainStep[3] // viral weight
0 domainStart[3]
0 domainStop[3]
-----see-the-bottom-for-a-check-of-included-positions------
0 included_parts // 0=Giege,1=E.coli,2=S.cerevisiae,3=blocks,4=Lin,5=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)
--------------------if-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
--------------------if-included_parts=4--------------------
0 ARE_SITES_UBIQUITOUS
0 ARE_SITES_NEAR_UBIQUITOUS
1 ARE_SITES_ISOTYPE_DISCRIMINATORS
0 ARE_SITES_CLADE_ISOTYPE_DISCRIMINATORS
0 ARE_SITES_ISOTYPE_SPECIFIC
0 ARE_SITES_TERTIARY_INTERACTING
0 ARE_SITES_A_BOX
0 ARE_SITES_B_BOX
--------------------if-included_parts=5--------------------
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'
1111111111111 Variable loop 5'->3'
1111111111 3'->5'
111111111111 T-arm 5'->3'
11111 3'->5'
333 a check of consistency
---------------a-check-of-included-positions---------------
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:1111111111111 T-arm:111111111111
111111 1111111111 11111
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