[Bioperl-l] Re mote Blast and Report

gopu_36 gopu_36 at yahoo.com
Tue Mar 3 09:36:53 EST 2009


I am kind of new to bioperl and will definitely check the version before I
start. I have a very similar situation to run remote blast but against
refseq database. I have a set of accession numbers for which I am intending
to run remote blast and parse the results. I was looking for some example to
blast against refsef. Hence do I have to modify as below?

$prog = "blastn";
$db = "refseq_rna";

My next doubt is since I have around 800 ACCESSION nos, do I have to
instantiate the below line that many times inside the loop?

$remoteBlast = Bio::Tools::Run::RemoteBlast->new(-prog => $prog,
                         -data => $db,
                         -expect => $e_val
                         -readmethod => 'Blast');

Thanks and Regards.

Ocar Campos-2 wrote:
> Hello:
>    I'm working in a script to remote blast a file with some sequences, I
> already got the part of sending the query to blast, but I do not get the
> idea of how retrieve a txt report, I mean, like the one you get by running
> a
> blast via web and you can read in a plane text editor.
> This is what I've done so far:
> use Bio::Tools::Run::RemoteBlast;
> use Bio::SearchIO;
> $prog = "tblastx";
> $db = "nr";
> $e_val = "1e-10";
> $remoteBlast = Bio::Tools::Run::RemoteBlast->new(-prog => $prog,
>                          -data => $db,
>                          -expect => $e_val
>                          -readmethod => 'Blast');
> #I select the file to make que query and do the blast.
> $infile = 'file.input.fasta';
> $r = $remoteBlast->submit_blast($infile);
> #this should be the report i get.
> $outfile = 'got.output';
> further than this I've tried some things but none of them work, anybody
> who
> could give an idea of how retrieving the plane text reports please?
> Cheers.
> O'car
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