[Biopython] remote blast against SRA database with biopython

[Fields, Christopher J]

Does the SRA blast database  show up in eutils einfo?

Chris


-------- Original message --------
From: Peter Cock
Date:12/21/2014 8:47 AM (GMT-06:00)
To: assaf www
Cc: Biopython Mailing List
Subject: Re: [Biopython] remote blast against SRA database with biopython

I was hoping it could be done with BLAST+ and the -remote option,
but that doesn't seem to work - maybe I have guessing the SRA
database name wrong?

$ blastn -query example -db sra -max_target_seqs 3 -outfmt 6 -remote
Warning: Error initializing remote BLAST database data loader:
Nucleotide BLAST database 'sra' does not exist in the NCBI servers
BLAST Database error: 'sra' not found on NCBI servers.

And:

$ blastn -query example.fasta -db SRA -max_target_seqs 3 -outfmt 6 -remote
Warning: Error initializing remote BLAST database data loader:
Nucleotide BLAST database 'SRA' does not exist in the NCBI servers
BLAST Database error: 'SRA' not found on NCBI servers.

In terms of the Biopython QBLAST function, that now uses
http://blast.ncbi.nlm.nih.gov/Blast.cgi internally, but does not
set the BLAST_SPEC parameter which is not officially in the
docmentation: http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html

Either that documentation is out of date, or using this would
be unofficial... but you could try extending that function?

Regards,

Peter


On Sun, Dec 21, 2014 at 11:09 AM, assaf www <assafwww at gmail.com> wrote:
> hi there,
> I would like to use remote blast against SRA database
> (http://www.ncbi.nlm.nih.gov/sra) with biopython, for specific
> experiments
>
> on the NCBI blast it is done from:
> https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=SRA&DB_GROUP=Exp
>
> do you maybe have and idea whether this can be done with biopython ?
> for example with NCBIWWW.qblast() or otherwise ?
>
> thanks a lot
> Assaf
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