General guidelines for the molecular basis of functional variation are presented while focused on the rotating circular genetic code and allowable exchanges that make it resistant to genetic diseases under normal conditions.
The rules of variation, bioinformatics aids for preventative medicine, are:
(1) same position in the four quadrants for hydrophobic codons,
(2) same or contiguous position in two quadrants for synonymous or related codons, and
(3) same quadrant for equivalent codons.
To preserve protein function, amino acid exchange according to
the first rule takes into account the positional homology of essential hydrophobic amino acids with every codon with a central uracil in the four quadrants,
the second rule includes codons for identical, acidic, or their amidic amino acids present in two quadrants, and
the third rule, the smaller, aromatic, stop codons, and basic amino acids, each in proximity within a 90 degree angle.
I also define codifying genes and palindromati, CTCGTGCCGAATTCGGCACGAG
Please cite this article as:
Castro-Chavez, F., The rules of variation: Amino acid exchange according to the rotating circular genetic code. J. Theor. Biol. (2010), 264(3):711-721., doi:10.1016/j.jtbi.2010.03.046
My earlier work on the palindromati contaminant can be found at:
I just submitted for consideration its 2010 update.
Here is the abstract, appeared on May, 2011, with the sequel of my studies on the genetic code!:
Castro-Chavez F. The Rules of Variation Expanded, Implications for the Research on Compatible Genomics. Biosemiotics. DOI: 10.1007/s12304-011-9118-0
If you are interested in the practical development of these rules of variation that I found in the rotating circular genetic code and in my work to improve the stringency of the nucleotide database filters, please let me know. Do you live in Houston and are interested in sponsoring my work? (My personal email is within the title link, thanks!)