[Bioperl-l] Re mote Blast and Report

Ocar Campos ocarnorsk138 at gmail.com
Tue Mar 3 10:40:44 EST 2009


Hello:

According to the documentation, depending on the database you want to use,
you modify the parameter, so what you did I think it should work, there is a
list of databases you can remoteblast and that is this one:
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html
I think General Databases is where you should search.

About the 800 Accession Numbers, wether you have the accesion numbers all in
one file or in different files, i think the creation of the object should
work doing it only once, what you should have in the loop is the line that
sends the file to blast, and the lines that parse the report, this only if
you have the accession numbers in more than one file.

Hope it helps.

Cheers

O'car Campos C.
Bioinformatics Engineering Student.
Universidad de Talca.


--
2009/3/3 gopu_36 <gopu_36 at yahoo.com>

>
> Hi,
>
> 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
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
> --
> View this message in context:
> http://www.nabble.com/Remote-Blast-and-Report-tp22214949p22309761.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


More information about the Bioperl-l mailing list