[Bioperl-l] Get GIs from Taxonomy ID

[shalabh sharma]

Hi Veronica,
                   You can also download the refseq release catalog.
ftp://ftp.ncbi.nih.gov/refseq/release/release-catalog/

 It contains all the information like GI and taxaIDs.
With the help of a simple script you can parse the required information.
Hope this helps.

Thanks
Shalabh Sharma



On Thu, Jun 10, 2010 at 4:00 PM, Dave Messina <David.Messina at sbc.su.se>wrote:

> 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_query
>
> 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
> >
> >
> >
> >
> > _________________________________________________________________
> > Hotmail is redefining busy with tools for the New Busy. Get more from
> your inbox.
> >
> http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>