Question: Is there any pairing info Genome <-> Plasmid in Genbank available?
0
gravatar for mschmid
3.4 years ago by
mschmid90
Switzerland
mschmid90 wrote:

If I have a bacterial genome in Genbank, how do I find the "corresponding" Plasmid? I am talking about projects where people sequenced the Genome and the Plasmids of a certain species.

 

Is there any specific information for that? Or do I have to infere it from the names? If there is any info on that: can the "matching" be automated?

genbank plasmid genome • 1.0k views
ADD COMMENTlink modified 3.4 years ago by piet1.6k • written 3.4 years ago by mschmid90
1
gravatar for piet
3.4 years ago by
piet1.6k
planet earth
piet1.6k wrote:

The sequences of all replicons of a bacterial isolate are linked to a common entry in the taxonomy database, and to a common entry in the biosample database. The genome of a bacterial cell may comprise several replicons, but the number of plasmids may vary within a species. Plasmids usually encode non-essential genes, and they can be acquired or lost.

If the accession of a sequence starts with AP, CP or BA, it is a complete replicon and it always has an associated entry in the taxonomy database. The entry in the taxonomy database refers to the bacterial isolate which has been sequenced, it is a sub-species entry. Example: pathogenic "Escherichia coli O157:H7 str. Sakai" having one chromosome and two plasmids

All newer full bacterial sequences are also linked a an associated entry in the biosample database. You can then use the biosample ID to find all replicons belonging to an isolate. Example: "Staphylococcus warneri SG" has one chromosome and 8 plasmids:

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by piet1.6k

Great, this already helps me a lot!

So if I automatically want to check if there is a plasmid found in the same project can I use NCBI's entrez?

If yes, could I find the Biosample entry via the accession number and from there the sequences associated? Would that work? Or what else would be a good automated search strategie?

ADD REPLYlink written 3.4 years ago by mschmid90

Yes, you can use Entrez esearch and elink to find the biosample assoziated with a given accession, and then vice visa all the nucleotide sequences assoziated with that biosample. 

ADD REPLYlink written 3.4 years ago by piet1.6k
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