Annotate plasmids with custom database + visualization

Question

[quimvipu1994]

Hi everyone,

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,

Quim

[GenoMax]

created a little database in ".fasta" format.

Fasta format is purely for sequence. What kind of database are you referring to?

[quimvipu1994]

I am just taking the name and the sequence of the desired genes and putting them on a file, and I was just wondering If it could be possible to use this "database" I have created to annotate my plasmids.

[GenoMax]

Ah I see. You have created a "reference" a multi-fasta sequence file of genes you are interested in. You could now create a blast database (makeblastdb) from this file and then blast your plasmids against this database to locate where these genes are in your plasmids (this process can also be done in reverse, if you wish).

You could also do mauve alignments of your plasmids (assuming they are related) to see how they relate to each other.

Answer 1

[Mensur Dlakic]

PlasMapper has most of the features you want. It will find features automatically (genes, promoters, terminators) or you can specify coordinates.

I like GENtle as well, but it takes a while to learn. It has many more features than just visualization, including virtual PCR and cloning (both restriction digestion and ligation). It has a local SQL database so you can keep record of your constructs. To give you a feel for its visualization features, below is an example image of one of my plasmid constructs.