Question: Search only plasmids from NT database using local BLAST
0
gravatar for Prakki Rama
2.4 years ago by
Prakki Rama2.4k
Singapore
Prakki Rama2.4k wrote:

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.

plasmid nt assembly ncbi • 822 views
ADD COMMENTlink written 2.4 years ago by Prakki Rama2.4k
1

You should have a look here.

ADD REPLYlink written 2.4 years ago by erwan.scaon810

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

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Prakki Rama2.4k

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.

ADD REPLYlink written 2.4 years ago by erwan.scaon810

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...:)

ADD REPLYlink written 2.4 years ago by Prakki Rama2.4k
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