[Bioperl-l] Get GIs from Taxonomy ID

[Smithies, Russell]

Eutils will do it with the right query:




use Bio::DB::EUtilities;
 
my $factory = Bio::DB::EUtilities->new(-eutil => 'esearch',
                         -db => 'nucleotide',
                         -term => 'txid9940[Organism:noexp]',
                         -email => 'mymail at foo.bar',
                         -retmax => 1000000);

# query hits
print "Count = ",$factory->get_count,"\n";
# UIDs
my @ids = $factory->get_ids;


--Russell


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Dave Messina
> Sent: Friday, 11 June 2010 8:01 a.m.
> To: armendarez77 at hotmail.com
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID
> 
> Hi Veronica,
> 
> These days when you run BLAST at the NCBI server, you're running BLAST+,
> which is their complete rewrite of (and replacement for) BLAST.
> 
> You can also download BLAST+ and do pretty much everything on your local
> machine that you can do on their server, including limit by taxonomy.
> 
> I think this is the right parameter:
> 
> 	http://www.ncbi.nlm.nih.gov/blast/html/blastcgihelp.html#entrez_que
> ry
> 
> Incidentally, BLAST+ has this awesome feature whereby you can, from the
> command line, run searches remotely on their server against their
> databases from the command line, just by adding the --remote flag.
> 
> 
> (You can run BLAST+ via the BioPerl wrapper module StandAloneBlastPlus, by
> the way.)
> 
> Dave
> 
> 
> 
> On Jun 10, 2010, at 4:54 PM, <armendarez77 at hotmail.com> wrote:
> 
> >
> > Hello,
> >
> > Is there a BioPerl method that will give a list of GIs for a specified
> NCBI taxonomy Id?
> >
> > I've previously tried using Urlapi to BLAST primers against the nr
> database on the NCBI server, but recently I keep getting a
> > 'Bad Gateway' error.  While my system admin is looking into this, I've
> > decided to go another route.  Therefore, I've downloaded the NCBI nr
> database.
> >
> > The problem I've run into is restricting the BLAST against the nr
> database to a subset of sequences.  The NCBI Blast tools have an option (-
> l) that does this, but it requires a list of GI's.
> >
> > When I was using Urlapi, I restricted sequences using Taxonomy Ids
> (Entrez Query).  Therefore, is there a way to get all GIs within a
> Taxonomy Id?  I've seen that woth Bio::Taxonomy I can give a GI and get a
> Tax Id, but not the reverse.
> >
> >
> > Thank you,
> >
> > Veronica
> >
> >
> >
> >
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