RESULTS

 

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

 

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 in-reality, is updated after each start of tRNALab in dependence on a parameter included_parts.)

Two compilations of tRNA genes were examined for control: 1) the Leipzig database and 2) the database by USCS. Some preliminary computations have also been performed with tRNAs provided by the Leipzig database and 3) the Poznan database.

Let each file whose hyperling follows after some 'settings' below, e.g., abe_L_classifications, abe_L_chronologies, etc., 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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The Poznan database of tRNAs:

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

When tRNAs, not tRNA genes as above, of only Homo sapiens are included in my computations and the modified nucleotides of tRNAs are distinguished, then the following promising results are obtained:

Data = e_P_dataR

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