Scott Markel | 14 May 18:18 2014

Re: remoteblast

In this case the code change is straightforward and doesn't require any change to
Bio::Tools::Run::RemoteBlast.  The constructor can take a URL_BASE argument, so just pass in the new URL
(  This will overwrite the old URL
( hard-coded in Bio::Tools::Run::RemoteBlast.  We
made this change to the remote BLAST components in the Pipeline Pilot Sequence Analysis collection and
things have been fine.

    my  <at> parameters = ("-prog"       => $program,
                      "-data"       => $database,
                      "-readmethod" => 'xml',
                      "-URL_BASE"   => $url);

    my $blastFactory = Bio::Tools::Run::RemoteBlast->new( <at> parameters);

Hope this helps.


Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel <at>
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-----Original Message-----
From: bioperl-l-bounces <at> [mailto:bioperl-l-bounces <at>] On
Behalf Of Jason Stajich
Sent: Wednesday, 14 May 14 2014 7:49 AM
To: Jolyon Holdstock
Cc: bioperl-l <at>
Subject: Re: [Bioperl-l] remoteblast

So the BLAST services changed - not sure if we will still even support perl
based - it will require a developer tracking and testing to the new NCBI
resources since the have discontinued the older submission CGI resource.

You can run remote blast with commandline tool from NCBI as an alternative.

I think we will need to have a developer volunteer who wants to keep
working on tracking the webservices for NCBI to keep this module working.


Jason Stajich
jason.stajich <at>

On Thu, May 8, 2014 at 8:34 AM, Jolyon Holdstock
<Jolyon.Holdstock <at>>wrote:

> Hi,
> I have a script that runs blast jobs against the databases at the NCBI.
> I use the  Bio::Tools::Run::RemoteBlast module for the blasting.
> It was working but is not now.
> The following is an example of the response I now get:
> --------------------- WARNING ---------------------
> MSG: req was POST
> User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.006901
> Content-Length: 788
> Content-Type: application/x-www-form-urlencoded
> <html>
> <head><title>An Error Occurred</title></head>
> <body>
> <h1>An Error Occurred</h1>
> <p>301 Moved Permanently</p>
> </body>
> </html>
> ---------------------------------------------------
> Can anyone suggest a fix?
> Thanks,
> Jolyon
> Dr. Jolyon Holdstock,
> Oxford Gene Technology
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