[Bioperl-l] Get GIs from Taxonomy ID
cjfields at illinois.edu
Thu Jun 10 17:35:48 EDT 2010
You can get up-to-date files mapping GI to TaxID here (nr and nt):
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;
>> -----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:
>> 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.)
>> On Jun 10, 2010, at 4:54 PM, <armendarez77 at hotmail.com> wrote:
>>> 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
>>> 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,
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>>> Bioperl-l at lists.open-bio.org
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