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Comparative Genomic Analysis

Hello

I am doing comparative genomic analysis between 50 genomes of a bacterial species. Among these 50 genomes some contains a plasmid and rest do not contain a plasmid. Should I include the plasmid in comparative studies or not?

Thanks!

genome sequence

It depends on your question. I don't think that chromosomal genes will be found in plasmids but maybe the plasmid genes are of interest.

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