Runs of Amino Acids in Peptides are Strongly Influenced by Choice of Subsets

D. Digby and W. Seffens (USA)


Genetic code, subgroups, sequence runs


Biological relevance was investigated for a natural sub grouping of the genetic code into three subsets, based upon association of reverse-complementary codons. Runs of amino acids were counted, a run being defined as any contiguous sequence of amino acids belonging to the same subset of the genetic code. Peptide sequences were analyzed by the “runs test” algorithm, which evaluates the statistical deviation of the number of actual runs, from the number expected from random sequences of the same elements. Many random sub-groupings of the genetic code were constructed, each resembling the natural sub grouping in being composed of exactly three subsets. Some exceptional random sub-groupings had skew and/or standard deviation values exceeding those of the natural sub-grouping. For each exceptional sub-grouping, every possible pair of amino acids was examined for relative sub-group membership. For each pair, the number of sub groupings was counted in which both members of the pair belonged to the same sub-group. For most pairs, this was approximately the one third to be expected in a random distribution. For several pairs, the count was significantly greater or less than expected, meaning that these two amino acids were separated into different sub-groups more or less often than expected. In particular, glutamine and serine were always separated.

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