I am analysing two categories of protein coding genes comparing their relative characteristics. What I am observing is that one of these, in comparison to the other, is enriched in pyrimidine runs (two ore more consecutive pyrimidines). I have counted the number of these runs (I do not call them dimers because I have no data underlining a cross-link between two or more pyrimidine bases) per protein coding-gene performing then a Mann Whitney test that indicates that one of these two group of genes is enriched with respect to the other. I am hypothesising that this enrichment could be an early indicator of DNA to undergo local conformation changes. By your experience, could this hypothesis be reliable or I am totally misleading what I am observing?

  • $\begingroup$ I find it difficult to understand your question. You talk about comparing proteins but refer to the nucleic acid base pyrimidine. Are you talking about the DNA sequences of their genes? If so, two consecutive pyrimidines are extremely common as they occur in 24 of the 64 codons. And when you say “categories” of proteins quite what do you mean by categories? The same protein in different organisms, protein kinases v. Immunoglobulins, or what? And you suddenly mention clusters — of what? You need to be much clearer if anyone is going to help you. $\endgroup$ – David Oct 12 '20 at 9:26
  • $\begingroup$ I edit my question you are right $\endgroup$ – Firingam Oct 12 '20 at 9:30
  • $\begingroup$ Basically, I am comparing protein coding genes with and without tandem repeats investigating why we have in some these repetitions (at amino acid level) and why not in others. You pointed an important detail about codon usage that already helped me. $\endgroup$ – Firingam Oct 12 '20 at 9:37

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