[Bioperl-l] Remote Blast question.

[Ralf Sigmund]

i am also a newbie to bioperl.
i wrote a simple blast parser using blastcl3 output before, however i could
only parse for the hit Accession number and score. Now I would like to
extract the aligned sequences' borders.
i wonder if i could do better with Bio::Tools::Run::RemoteBlast.

i tried to understand the modules' usage by looking at the inline
documentation, but now i wonder how do i set @params ?

i tried:

@params = ('program' => 'blastn', 'database' => 'nr');

but this results in the runtime msg:
-------------------- WARNING ---------------------
MSG: trying to set program to an invalid program name (program) --
defaulting to blastp


if i use a empty @params:

------------------------------------------------------------------
use Bio::SeqIO;
use Bio::Seq;
use Bio::Tools::Run::RemoteBlast;
@params = ();
$input = Bio::Seq->new('-id'=>"test query",
                         '-seq'=>"ACTAAGTGGGGG");
$factory = Bio::Tools::Run::RemoteBlast->new(@params);

$blast_report = $factory->runblast($input);
-------------------------------------------------------------------
i allways get this error:

Can't locate object method "runblast" via package
"Bio::Tools::Run::RemoteBlast" (perhaps you forgot to load
"Bio::Tools::Run::RemoteBlast"?) at H:\test4.pl line 9.

thanks for any help ralf