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<div>Does the SRA blast database show up in eutils einfo?</div>
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<div>Chris</div>
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<br>
<div>-------- Original message --------</div>
<div>From: Peter Cock </div>
<div>Date:12/21/2014 8:47 AM (GMT-06:00) </div>
<div>To: assaf www </div>
<div>Cc: Biopython Mailing List </div>
<div>Subject: Re: [Biopython] remote blast against SRA database with biopython </div>
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<div class="PlainText">I was hoping it could be done with BLAST+ and the -remote option,<br>
but that doesn't seem to work - maybe I have guessing the SRA<br>
database name wrong?<br>
<br>
$ blastn -query example -db sra -max_target_seqs 3 -outfmt 6 -remote<br>
Warning: Error initializing remote BLAST database data loader:<br>
Nucleotide BLAST database 'sra' does not exist in the NCBI servers<br>
BLAST Database error: 'sra' not found on NCBI servers.<br>
<br>
And:<br>
<br>
$ blastn -query example.fasta -db SRA -max_target_seqs 3 -outfmt 6 -remote<br>
Warning: Error initializing remote BLAST database data loader:<br>
Nucleotide BLAST database 'SRA' does not exist in the NCBI servers<br>
BLAST Database error: 'SRA' not found on NCBI servers.<br>
<br>
In terms of the Biopython QBLAST function, that now uses<br>
<a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi">http://blast.ncbi.nlm.nih.gov/Blast.cgi</a> internally, but does not<br>
set the BLAST_SPEC parameter which is not officially in the<br>
docmentation: <a href="http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html">http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html</a><br>
<br>
Either that documentation is out of date, or using this would<br>
be unofficial... but you could try extending that function?<br>
<br>
Regards,<br>
<br>
Peter<br>
<br>
<br>
On Sun, Dec 21, 2014 at 11:09 AM, assaf www <assafwww@gmail.com> wrote:<br>
> hi there,<br>
> I would like to use remote blast against SRA database<br>
> (<a href="http://www.ncbi.nlm.nih.gov/sra">http://www.ncbi.nlm.nih.gov/sra</a>) with biopython, for specific<br>
> experiments<br>
><br>
> on the NCBI blast it is done from:<br>
> <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=SRA&DB_GROUP=Exp">
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=SRA&DB_GROUP=Exp</a><br>
><br>
> do you maybe have and idea whether this can be done with biopython ?<br>
> for example with NCBIWWW.qblast() or otherwise ?<br>
><br>
> thanks a lot<br>
> Assaf<br>
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