I have assembled 3 plasmids containing blaNDM-7 carbapenemase using Flye with --plasmids flag and Oxford Nanopore reads. Prokka annotation did not work well for the plasmids, so I decided to Blast one of the sequences.
I have retrieved some genes from the best match and created a little database in ".fasta" format.
So, I have my plasmids in ".fasta" files and the genes in another ".fasta" file. How could I annotate my plasmids using this little database I have created? And how could I visualize the comparison of the 3 plasmids once the annotation is performed?
Thank you so much,