The amino acids that are forbidden to represent classes: G P Group 1: VA Group 2: CFWX Group 3: TNMIKR Group 4: EQD Group 5: HYSL Group 6: G Group 7: P Chronology: MIVCQHTWKYGNFAXPDESRL ch_p_sim: 18.5766 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P Q Group 1: WFXC Group 2: TIMNRK Group 3: YHSL Group 4: EDQ Group 5: VA Group 6: G Group 7: P Chronology: MIWHEVTCKYGNFAXQDPSRL ch_p_sim: 18.5748 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P Q H Group 1: YHSL Group 2: AV Group 3: QED Group 4: NMITRK Group 5: CFWX Group 6: G Group 7: P Chronology: MIYAECTKHWGNFVXQDPSRL ch_p_sim: 18.5731 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P Q H Y Group 1: IMNKTRX Group 2: YLSW Group 3: FHC Group 4: VA Group 5: QED Group 6: G Group 7: P Chronology: MIWCVETKHYGNFAQXDPSRL ch_p_sim: 18.5493 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P Q H Y W Group 1: AV Group 2: RMKINT Group 3: EDQ Group 4: CWX Group 5: HSFLY Group 6: G Group 7: P Chronology: MIAECFTKHWGNYVXQDPRSL ch_p_sim: 18.5397 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P Q H Y C Group 1: CWFLS Group 2: IMTNRK Group 3: HYQ Group 4: EDX Group 5: VA Group 6: G Group 7: P Chronology: MIWEVTCKYHGNFAXQDPRSL ch_p_sim: 18.5087 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P Q H Y E Group 1: CSLF Group 2: EYH Group 3: TKINMR Group 4: VDA Group 5: QWX Group 6: G Group 7: P Chronology: MICVWTKYHQFNGAXPDERSL ch_p_sim: 18.4721 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P Q H E Group 1: R Group 2: YQHE Group 3: VDA Group 4: TINKMX Group 5: LCSFW Group 6: G Group 7: P Chronology: MIRYVCTKHWGNFAXDQEPSL ch_p_sim: 18.4735 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P Q H E R Group 1: NIMKRT Group 2: QWE Group 3: VAD Group 4: FCX Group 5: LSYH Group 6: G Group 7: P Chronology: MIWVCYTKHQFNGAXPDESRL ch_p_sim: 18.463 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P Q H E C Group 1: MTIKNXR Group 2: VAD Group 3: YHCF Group 4: SL Group 5: QWE Group 6: G Group 7: P Chronology: MIVYSWTKHQNFAPXCDEGRL ch_p_sim: 18.4053 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P Q H C Group 1: TKINMR Group 2: EQD Group 3: HYSL Group 4: VA Group 5: CWFX Group 6: G Group 7: P Chronology: MIEYVWTKCHGNFAXQDPSRL ch_p_sim: 18.5021 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P Q H C W Group 1: LSYH Group 2: AV Group 3: EDX Group 4: TINMKFR Group 5: QWC Group 6: G Group 7: P Chronology: MIYAETKHWCGNVXFQDPSRL ch_p_sim: 18.4998 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P Q E Group 1: WXFC Group 2: RKTIMN Group 3: AV Group 4: LSY Group 5: QHED Group 6: G Group 7: P Chronology: MICAYHTKWQGNFVXPDESRL ch_p_sim: 18.5457 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P Q E C Group 1: AV Group 2: YWXF Group 3: HQDE Group 4: IMTKNCR Group 5: SL Group 6: G Group 7: P Chronology: MIAYHSTKWQNFVXPDCEGRL ch_p_sim: 18.4824 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P Q E C S Group 1: RNITMK Group 2: EHDQ Group 3: FWCX Group 4: VA Group 5: SYL Group 6: G Group 7: P Chronology: MIHWVYTKCQGNFAXPDESRL ch_p_sim: 18.4782 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P Q E Y Group 1: CFX Group 2: VA Group 3: EHDQ Group 4: WYLS Group 5: RNTKMI Group 6: G Group 7: P Chronology: MICVHWTKYQFNGAXPDESRL ch_p_sim: 18.5338 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P Q E Y W Group 1: YSLF Group 2: WCX Group 3: QHED Group 4: AV Group 5: ITNKRM Group 6: G Group 7: P Chronology: MIFCHATKWQYNGVXPDESRL ch_p_sim: 18.5293 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P H Group 1: NKTMRI Group 2: VA Group 3: XCFW Group 4: EQD Group 5: HLYS Group 6: G Group 7: P Chronology: MIVCQYTKHWGNFAXPDESRL ch_p_sim: 18.5749 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P H C Group 1: AV Group 2: HYSL Group 3: TIKMNR Group 4: EDQ Group 5: WXCF Group 6: G Group 7: P Chronology: MIAYQWTKCHGNFVXPDESRL ch_p_sim: 18.5038 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P H C Y Group 1: AV Group 2: FLSCW Group 3: YH Group 4: QED Group 5: TRIMNKX Group 6: G Group 7: P Chronology: MIAWQTCKYHGNFVPXDERSL ch_p_sim: 18.5035 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P H C Y W Group 1: EDQ Group 2: TNIMKRX Group 3: VA Group 4: HYW Group 5: SCFL Group 6: G Group 7: P Chronology: MIQVFTKCYHGNWAPXDESRL ch_p_sim: 18.4924 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P H C Y T Group 1: HY Group 2: VA Group 3: QED Group 4: WLSCF Group 5: ITMRKNX Group 6: G Group 7: P Chronology: MIVQWKTCYHGNFAPXDERSL ch_p_sim: 18.5009 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P H C W Group 1: TIMRNFK Group 2: VAD Group 3: EQX Group 4: YHLS Group 5: WC Group 6: G Group 7: P Chronology: MIVQYTKHWCGNAXFPDESRL ch_p_sim: 18.4983 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P H C W T Group 1: NTIMRKF Group 2: EXQ Group 3: LSYH Group 4: VAD Group 5: WC Group 6: G Group 7: P Chronology: MIQYVKTHWCGNAXFPDESRL ch_p_sim: 18.4964 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P H Y Group 1: SLYW Group 2: FHC Group 3: VA Group 4: EQD Group 5: ITKNMRX Group 6: G Group 7: P Chronology: MIWCVQTKHYGNFAPXDESRL ch_p_sim: 18.5515 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P H Y W Group 1: IMNRKT Group 2: FYHLS Group 3: WCX Group 4: EQD Group 5: VA Group 6: G Group 7: P Chronology: MIFCQVTKHWGNYAXPDERSL ch_p_sim: 18.5415 -------------------------------------------------------------------------- The amino acids that are forbidden to represent classes: G P H Y W F Group 1: EQD Group 2: MTIKRNX Group 3: HYF Group 4: AV Group 5: SLCW Group 6: G Group 7: P Chronology: MIQACTWKYHGNFVPXDESRL ch_p_sim: 18.5086 -------------------------------------------------------------------------- 1 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 ----------------------------------------------------------- 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 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 0 NONSTANDARD_ASSIGNMENTS // are 0=ignored or 1=processed according to amino acids ----------------------------------------------------------- 5 numOfOptimizableGroups 2 numOfOneElementGroups G P oneElementGroups 1 groupWeight // vs. familyWeight=1 ----------------------------------------------------------- 0 numOfNonStartAAs nonStartAAs ----------------------------------------------------------- 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 ----------------------------------------------------------- 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 10 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 3 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: 01111100 D-arm:00110101000001000 00011111100 1101 Anticodon arm:0000000011111 Variable loop:1111111111111 T-arm:000000000000 100000 1111111111 00000 ----------------------------------------------------------- THE SIMULATION HAS FINISHED. -------------------------------------------------