[Bioperl-l] Get GIs from Taxonomy ID

Dave Messina David.Messina at sbc.su.se
Thu Jun 10 16:00:49 EDT 2010

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:

> 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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