[Bioperl-l] Fwd: RemoteBlast has an upper limit fo 100 returned hits ?

[Jason Stajich]

Philip - best to ask on the mailing list. fwding it on.
-jason
Begin forwarded message:

> From: "Xiang, Philip" <philip.xiang at roche.com>
> Date: February 18, 2009 12:37:23 PM PST
> To: <jason at bioperl.org>
> Subject: RemoteBlast has an upper limit fo 100 returned hits ?
>
> Hi Jason,
>
>
>
> I don't seem to be able to get more than 100 sequences returned with
> Bio::Tools::Run RemoteBlast.
>
> I get 10 hits returned with the following piece of code.
>
>  my @params = ( '-prog' => 'blastn',
>
>         '-data' => 'nr',
>
>         '-expect' => '1e-10',
>
>         '-descriptions' => 10,
>
>         '-alignments' => 10,
>
>         '-readmethod' => 'SearchIO' );
>
>  my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>
>  my $r = $factory->submit_blast($input);
>
>
>
> But I get only 100 hits returned if I change the code to:
> '-descriptions' => 10000, '-alignments' => 10000, even though the  
> query
> fetches a lot more hits on NCBI BLAST web interface.
>
> What did I do wrong?
>
> Thank you in advance for your help!
>
>       Phil Xiang
>
>       Phone: 925.730.8709
>
>
>

Jason Stajich
jason at bioperl.org