RESULTS

 

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

 

Input parameters are read from settings.txt each time my program tRNALab is started. They are also listed at the end of each output file. All input parameters in capitals are Boolean. #class means the prescribed number of classificatory groups.

Let each file whose hyperling follows just after some 'settings' below, i.e., abe_L_classifications, abe_L_nonGlobAAs, abe_L_nonStartAAs, abe_L_FindLUCA, and abe_C_FindScores, be called a listing of main results (MR).

Any presence of classifications 1) XMITNKRF, 2) HQE, 3) DAV, 4) LSYCZW, 5) G, and 6) P (Eq. 2) for #class = 6 or 1) XMITNKRF, 2) QE, 3) DAV, 4) HLSZ, 5) YWC, 6) G, and 7) P (Eq. 4) for #class = 7 is indicated by + on this page and in MRs for the Leipzig database.

Any presence of classifications 1) XMITNKR, 2) HQE, 3) DAV, 4) FLSYCZW, 5) G, and 6) P (Eq. 3a) for #class = 6 or 1) XMITNKR, 2) HQE, 3) DAV, 4) LSZ, 5) FYCW, 6) G, and 7) P (Eq. 5a) for #class = 7 is indicated by ++ on this page and in MRs for the Leipzig database.

Because the database by UCSC contains no tRNA genes of rare selenocysteine (SecZ), + and ++ mean the same, but without Z, for this database.

 

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

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The Leipzig database of tRNA genes:

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Non-standard assignments = 0 (false) (NS0):

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

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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

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The database of tRNA genes by UCSC:

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

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Non-standard assignments = 0 (false) (NS0):

Data = abe_C_dataD

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

Data = abe_C_dataD

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