Should we remove plasmid sequences for Whole genome Alignment
Hello there!!
Should we remove plasmid sequences from genome assemblies for Whole Genome alignment?
I want to perform Whole genome alignment among 20 bacterial genomes. of 20, only 5 genomes have plasmids in them while the rest have only chromosome.
Is it advisable to remove those plasmid sequences before proceeding to Whole genome alignment using Progressive mauve?
Thank You
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Better remove them cause plasmids are highly mobile elements.