[Bioperl-l] RemoteBlast and psiblast

Wed, 11 Sep 2002 12:56:32 +0300 (IDT)

Hi,
I have encountered the following error message while running a simple
remote blast script:

-------------------- WARNING ---------------------
MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
User-Agent: libwww-perl/5.64
Content-Length: 541
Content-Type: application/x-www-form-urlencoded

PROGRAM=blastp&QUERY=MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD&DATABASE=nr&SERVICE=plain&CMD=Put&EXPECT=1e-3&CDD_SEARCH=off&FORMAT_OBJECT=Alignment&COMPOSITION_BASED_STATISTICS=off&FILTER=L

<HTML>
<HEAD><TITLE>An Error Occurred</TITLE></HEAD>
<BODY>
<H1>An Error Occurred</H1>
500 Can't connect to www.ncbi.nlm.nih.gov:80 (Timeout)
</BODY>
</HTML>

---------------------------------------------------

while using the following script:

---
#!/usr/bin/perl -w
use Bio::SeqIO;
use Bio::Tools::Run::RemoteBlast;

my $Seq_in = Bio::SeqIO->new (-file => $ARGV[0], -format => 'fasta');
my $query = $Seq_in->next_seq();

my $factory = Bio::Tools::Run::RemoteBlast->new(
        '-prog'  => 'blastp',
        '-data' => 'nr',
        '-proxy' => 'http://wwwproxy.huji.ac.il:8080',
        _READMETHOD => "Blast"
        );

my $blast_report = $factory->submit_blast($query);
---

I don't think the problem is my proxy, because I can connect to the same
site (www.ncbi.nlm.nih.gov) through wget.

any idea what's going on? I'm using bioperl version 1.0.1, and perl
version 5.6.1 on Linux.

Thanks,
Hadas.