Bioperl: Re: question:bioperl remote blast error
Steve Chervitz
sac@neomorphic.com (Steve A. Chervitz)
Wed, 12 Jan 2000 03:41:51 -0800 (PST)
James,
I've just uploaded a patch for using the run_blast_remote.pl script on
the bio.perl.org ftp site:
ftp://bio.perl.org/pub/sac/blast/Bioperl-run-blast-patch.tar.gz
or
ftp://bio.perl.org/pub/sac/blast/Bioperl-run-blast-patch.zip
This permits BLAST analysis on the NCBI server. It's not an ideal
solution, but will do for now. Check out the README in this archive
for details.
The remote BLASTing script cannot be configured to use an alternative
site, but this could be added without too much trouble. If you need
to do this now, you can edit the server URL used in the Webblast.pm
module, but any alternative site must be compatible with the NCBI web
form.
Cheers,
Steve
--
Steve A. Chervitz
sac@neomorphic.com
James Tisdall writes:
> Hi,
> using
> ./run_blast_remote.pl -prog blastx -db nr seq2.fasta
> I get an error file jimseq.blastx2.nr.temp.html with contents
>
> <HEAD>
> <META HTTP-EQUIV=Refresh
> CONTENT=4;URL=http://www.ncbi.nlm.nih.gov/blast/blast.cgi>
> </HEAD>
> Forwarding your request to the new system
>
>
> Couldn't find a mention of this on mail list archives or docs.
> Apparently NCBI moved their service. Is there a way to configure
> bioperl to do blast remotely at ncbi or elsewhere?
>
> Many thanks,
>
> Jim
>
>
> --
> ----------------------------------------------------------------------
> James D. Tisdall Phone: (215) 728-3660
> The Fox Chase Cancer Center FAX: (215) 728-2513
> 7701 Burholme Avenue Email: JD_Tisdall@fccc.edu
> Philadelphia, Pennsylvania 19111 USA
>
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