In monkey pox genomes, around 6000 bp inverted repeats are found at both the ends. If we calculate the codon usage in such genomes, should we exclude one inverted repeat or Can we consider both repeats for calculation. Some say that if we consider both, it may lead to over estimation of codon usage. My question is ,"In reality, two repeats exist, then why should we exclude one repeat when we calculate codon usage bias in monkeypox genomes?....
Some say that we can include both repeats for calculation of codon usage bias...
Which is true?
Hi Rahul,
Yes you are right, sometimes you have the possibility to make calculation taking this possible bias in account or not and then compare.
In order to understand more about this kind of bias, please read this article:
Hockenberry, A. J., Sirer, M. I., Amaral, L. A. N., & Jewett, M. C. (2014). Quantifying Position-Dependent Codon Usage Bias. Molecular Biology and Evolution, 31(7), 1880–1893. http://doi.org/10.1093/molbev/msu126
Best
Dear Rahul,
This may be a late answer, but in my mind what you have to be careful of is to use only the regions used for coding proteins and not the full genome for you codon usage calculations ! the codon bias is only useful if you consider the protein coding part of the genome (ie open reading frames, or mRNA). So your question must be is there any protein coding genes in these inverted repeats, and if yes, then you must take them into account, twice if there are two functional copies of them. I am quite sure the poxvirus transcriptome is known ...
Cheers
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