Comparative Genomic Analysis

Question

[utkarsh.sood]

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!

[Asaf]

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.