I am doing the comparative analysis of a bacterial genus . Now, in the NCBI database, we have assemblies of this genus at different levels like contigs, scaffolds or complete genome. Now, complete genomes have separate plasmid sequences whereas there is no such demarcation (between main chromosome and plasmid) for assemblies at draft and scaffold level. Now, the problem is what file format i.e. gbk or .faa would be suitable for doing comparative genome analysis in this situation, where we have to compare assemblies at different levels. Regards Neeti Pandey