Search only plasmids from NT database using local BLAST

Question

[Prakki Rama]

Hi all,

May I know, if there is a way to search for only plasmids instead of whole NT database locally?

Many thanks in advance.

[erwan.scaon]

You should have a look here.

[Prakki Rama]

Thank you for reply @erwan.scaon. I will try the above link and come back.

[erwan.scaon]

Ps : If you are not using blast+ 2.8.0 & BLAST v5 databases (as mentionned in my link), you can still use the "-seqidlist" parameter from previous versions of blast+ :

-seqidlist <string>
Restrict search of database to list of SeqId's

With the "list of SeqId's" being all plasmids SeqId's in nt database.

[Prakki Rama]

Thanks erwan. Having a list of ids, would be straight forward task to extract and generate database, run blast. But actually, I do not have a list of plasmid ids. Basically, I just wanted to see what plasmids exists in my assembly. I am trying out the V5 database..Download in progress...:)