results

SIMULATIONS

The following simulations are described in my manuscript "A periodic diagram of the genetic code and a pendulum evolutionary law: towards a designer of code expanding".

Input parameters are loaded from settings.txt every time my program tRNALab is launched. They are also listed at the end of each output file. #class means the prescribed number of classificatory groups. All input parameters in capitals are Boolean. (The last section of settings.txt, entitled by a-check-of-included-positions, is updated after each start of tRNALab in dependence on the previous parameters.)

Two compilations of tRNA genes were examined for control: 1) the Leipzig database and 2) the database by USCS.

Any presence of classifications 1) XMITNKRF, 2) HQE, 3) DAV, 4) LSYCUW, 5) G, and 6) P (Eq. 2) for #class = 6 or 1) XMITNKRF, 2) QE, 3) DAV, 4) HLSU, 5) YWC, 6) G, and 7) P (Eq. 4) for #class = 7 is indicated by + on this page and in output listings.

Any presence of classifications 1) XMITNKR, 2) HQE, 3) DAV, 4) FLSYCUW, 5) G, and 6) P (Eq. 3a) for #class = 6 or 1) XMITNKR, 2) HQE, 3) DAV, 4) LSU, 5) FYCW, 6) G, and 7) P (Eq. 5a) for #class = 7 is indicated by ++ on this page and in output listings.

Functions: f0 = FindLUCA, f1 = FindScores, f2 = FindNonStartAAs, f3= FindNonGlobAAs, f4= GlobOptimizeGroups, and f5 = CompleteTestData.

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The Leipzig database of tRNA genes:

There are 37 tRNA genes with non-standard assignments in the Leipzig database, e.g., 14 tRNA genes of Ile are assigned to a codon AUG. These 37 tRNA genes are ignored in the following experiments.

Data = abe_L_dataD

#class = 4:
- 1) f4, sites = all (settings, abe_L_classifications , abe_L_setting_details, abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out )
#class = 5:
- 2) f4, sites = all (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out )
#class = 6:
- 3) f4, sites = all (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out ) Eq. 2 of the manuscript +
- 4) f3, sites = all (settings, abe_L_nonGlobAAs , job.out) ⇒ ¬Glob = CU is set as an input parameter of (8) ++
- 5) f3, sites = all, MX_MOVE_TOGETHER = 1 (settings, abe_L_nonGlobAAs , job.out ) ⇒ ¬Glob = CU ++
- 6) f3, sites = G3 (settings, abe_L_nonGlobAAs , job.out )
- 7) f3, sites = G3, MX_MOVE_TOGETHER = 1 (settings, abe_L_nonGlobAAs , job.out )
- 8) f4, sites = all, ¬Glob = CU (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out ) Eq. 3 ++
- 9) f2, sites = all (settings, abe_L_nonStartAAs) 7 ✕ +
- 10) f2, sites = all, MX_MOVE_TOGETHER = 1 (settings, abe_L_nonStartAAs) 9 ✕ +
#class = 7:
- 11) f4, sites = all (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out )
- 12) f3, sites = all (settings, abe_L_nonGlobAAs , job.out) ⇒ ¬Glob = CUH is set as an input parameter of (16) + !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
- 13) f3, sites = all, MX_MOVE_TOGETHER = 1 (settings, abe_L_nonGlobAAs , job.out ) ⇒ ¬Glob = CUH ++
- 14) f3, sites = G3 (settings, abe_L_nonGlobAAs , job.out )
- 15) f3, sites = G3, MX_MOVE_TOGETHER = 1 (settings, abe_L_nonGlobAAs , job.out ) +
- 16) f4, sites = all, ¬Glob = CUH (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out ) Eq. 5 ++
#class = 8:
- 17) f4, sites = all (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out )
#class = 9:
- 18) f4, sites = all (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out )
#class = 10:
- 19) f4, sites = all (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out )

Non-standard assignments = 1 (true) (NS1):

There are 37 tRNA genes with non-standard assignments in the Leipzig database, e.g., 14 tRNA genes of Ile are assigned to a codon AUG. They are treated as if they were assigned to a codon AUU in the following experiments. The rest of the non-standard assignments are treated analogically.

Data = abe_L_dataD

#class = 4:
- 20) f4, sites = all (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out )
#class = 5:
- 21) f4, sites = all (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out )
#class = 6:
- 22) f0, sites = all (settings, abe_L_FindLUCA)
- 23) f4, sites = all (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out ) Eq. 2 +
- 24) f3, sites = all (settings, abe_L_nonGlobAAs , job.out) ⇒ ¬Glob = CU is set as an input parameter of (28) ++
- 25) f3, sites = all, MX_MOVE_TOGETHER = 1 (settings, abe_L_nonGlobAAs , job.out) ⇒ ¬Glob = CU ++
- 26) f3, sites = G3 (settings, abe_L_nonGlobAAs , job.out ) +
- 27) f3, sites = G3, MX_MOVE_TOGETHER = 1 (settings, abe_L_nonGlobAAs , job.out ) +
- 28) f4, sites = all, ¬Glob = CU (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out ) Eq. 3-4 ++
- 29) f2, sites = all (settings, abe_L_nonStartAAs ) 7 ✕ +
- 30) f2, sites = all, MX_MOVE_TOGETHER = 1 (settings, abe_L_nonStartAAs ) 10 ✕ +
#class = 7:
- 31) f4, sites = all (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out )
- 32) f3, sites = all (settings, abe_L_nonGlobAAs , job.out) ⇒ ¬Glob = CUH is set as an input parameter of (36) ++
- 33) f3, sites = all, MX_MOVE_TOGETHER = 1 (settings, abe_L_nonGlobAAs , job.out) ⇒ ¬Glob = CUH ++
- 34) f3, sites = G3 (settings, abe_L_nonGlobAAs , job.out) +
- 35) f3, sites = G3, MX_MOVE_TOGETHER = 1 (settings, abe_L_nonGlobAAs , job.out) +
- 36) f4, sites = all, ¬Glob = CUH (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out ) Eq. 5, Extended Fig.1, Fig. 2 ++
#class = 8:
- 37) f4, sites = all (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out )
#class = 9:
- 38) f4, sites = all (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out )
#class = 10:
- 39) f4, sites = all (settings, abe_L_classifications , abe_L_chronologies, abe_L_p_simChart, abe_L_ch_p_simChart, job.out )

The database of tRNA genes by UCSC:

Please, keep in mind that this database contains no tRNA genes of rare selenocysteine (Sec ≡ U).

Data = abe_C_dataD

#class = 4:
- 40) f4, sites = G3, score ≧ 67, MX_MOVE_TOGETHER = 1 (settings, abe_C_classifications , abe_C_chronologies, abe_C_p_simChart, abe_C_ch_p_simChart, job.out )
#class = 5:
- 41) f4, sites = G3, score ≧ 67, MX_MOVE_TOGETHER = 1 (settings, abe_C_classifications , abe_C_chronologies, abe_C_p_simChart, abe_C_ch_p_simChart, job.out )
#class = 6:
- 42) f0, sites = all, score ≧ 67, MX_MOVE_TOGETHER = 1 (settings, abe_C_FindLUCA)
- 43) f1, sites = all, MX_MOVE_TOGETHER = 1 (settings, abe_C_FindScores) ⇒ score ≧ 67 is set as an input parameter of (40-42, 44-45, 49-60) ++
- 44) f1, sites = G3, MX_MOVE_TOGETHER = 1 (settings, abe_C_FindScores ) ⇒ score ≧ 67.5-69.5 ++
- 45) f4, sites = G3, score ≧ 67, MX_MOVE_TOGETHER = 1 (settings, abe_C_classifications , abe_C_chronologies, abe_C_p_simChart, abe_C_ch_p_simChart, job.out )
- 46) f3, sites = all, score ≧ 67 (settings, abe_C_nonGlobAAs , job.out )
- 47) f3, sites = all, score ≧ 67, MX_MOVE_TOGETHER = 1 (settings, abe_C_nonGlobAAs , job.out ) ⇒ ¬Glob = ∅ ++
- 48) f4, sites =all, score ≧ 67, MX_MOVE_TOGETHER = 1, ¬Glob = ∅ (settings, abe_C_classifications , abe_C_chronologies, abe_C_p_simChart, abe_C_ch_p_simChart, job.out ) ++ (will be added)
- 49) f3, sites = G3, score ≧ 67 (settings, abe_C_nonGlobAAs , job.out) ⇒ ¬Glob = Q ++
- 50) f3, sites = G3, score ≧ 67, MX_MOVE_TOGETHER = 1 (settings, abe_C_nonGlobAAs , job.out ) ⇒ ¬Glob = Q is set as an input parameter of (51) ++
- 51) f4, sites = G3, score ≧ 67, MX_MOVE_TOGETHER = 1, ¬Glob = Q (settings, abe_C_classifications , abe_C_chronologies, abe_C_p_simChart, abe_C_ch_p_simChart, job.out ) Eq. 6 ++
#class = 7:
- 52) f4: sites = G3, score ≧ 67, MX_MOVE_TOGETHER = 1 (settings, abe_C_classifications , abe_C_chronologies, abe_C_p_simChart, abe_C_ch_p_simChart, job.out )
- 53) f3: sites = all, score ≧ 67 (settings, abe_C_nonGlobAAs , job.out )
- 54) f3: sites = all, score ≧ 67, MX_MOVE_TOGETHER = 1 (settings, abe_C_nonGlobAAs , job.out)
- 55) f3: sites = G3, score ≧ 67 (settings, abe_C_nonGlobAAs , job.out )
- 56) f3: sites = G3, score ≧ 67, MX_MOVE_TOGETHER = 1 (settings, abe_C_nonGlobAAs , job.out) ⇒ ¬Glob = CQE is set as an input parameter of (57) ++
- 57) f4, sites = G3, score ≧ 67, MX_MOVE_TOGETHER = 1, ¬Glob = CQE (settings, abe_C_classifications , abe_C_chronologies, abe_C_p_simChart, abe_C_ch_p_simChart, job.out ) Eq. 7 ++
#class = 8:
- 58) f4: sites = G3, score ≧ 67, MX_MOVE_TOGETHER = 1 (settings, abe_C_classifications , abe_C_chronologies, abe_C_p_simChart, abe_C_ch_p_simChart, job.out )
#class = 9:
- 59) f4: sites = G3, score ≧ 67, MX_MOVE_TOGETHER = 1 (settings, abe_C_classifications , abe_C_chronologies, abe_C_p_simChart, abe_C_ch_p_simChart, job.out )
#class = 10:
- 60) f4: sites = G3, score ≧ 67, MX_MOVE_TOGETHER = 1 (settings, abe_C_classifications , abe_C_chronologies, abe_C_p_simChart, abe_C_ch_p_simChart, job.out )

Although there are 1271 tRNA genes with non-standard assignments in the database by UCSC provided that score ≧ 67, they are all assigned to Ile and do not significantly change results of our simulations. Therefore, we do not list them among the main simulations.