This is a test version of Biostars. For the public version, visit https://www.biostars.org.
tBLASTn search in wgs database: how to specify the organism?

Hi,

I'm interested in searching the wgs database for specific organisms as I can easily do on the website: enter image description here

But I seem to be unable to find a flag that would allow me to specify the taxid if I'm searching using the command line or Bio.Blast.NCBIWWW module. I'm trying to avoid downloading the database locally and getting an Error: (CArgException::eConstraint) Argument "taxids". Incompatible with argument: "remote" error from command line tblastn.

Am I missing something obvious or is it indeed impossible?

Thanks!

blast taxid
• 912 views • link
updated by GenoMax GenoMax • written by Nina • Nina

1 answer

You can't use taxids option with -remote. WGS database is not available for local download because of its size. So you will have to do this search online.

 -remote
   Execute search remotely?
    * Incompatible with:  gilist, seqidlist, taxids, taxidlist,
• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this