[Bioperl-l] Get GIs from Taxonomy ID

[Chris Fields]

You can get up-to-date files mapping GI to TaxID here (nr and nt):

ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/

chris

On Jun 10, 2010, at 4:11 PM, Smithies, Russell wrote:

> 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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>> 
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