[Bioperl-l] Remote Blast against RefSeq_mrna db (Bio::Tools::Run::RemoteBlast)

Fields, Christopher J cjfields at illinois.edu
Wed Oct 17 23:25:52 EDT 2012


The below script using Bio::DB::EUtilities will get you some results, all in nice readable XML output.  Unfortunately at the moment this is only given in NCBI's DocSum v2.0 (which we don't actively parse), so you will have to munge out the path for the database of interest.

(BTW, I think NCBI doing this is a great thing, at least it's searchable and kept up-to-date, we just need to actively start supporting it)

chris
---------------------------------------
#!/usr/bin/env perl
use Modern::Perl;
use Bio::DB::EUtilities;

my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                     -term  => '"refseq rna"',
                                     -email => 'cjfields at bioperl.org',
                                     -db    => 'blastdbinfo',
                                     -usehistory => 'y');

my $hist = $eutil->next_History || die "No history returned";

$eutil->set_parameters(-eutil => 'esummary',
                    -history => $hist,
                    -version => '1.0');

say $eutil->get_Response->content;




On Oct 17, 2012, at 8:47 PM, Malachy Campbell <campbell.malachy at gmail.com> wrote:

> Hello all,
> I would like to run a remote blast search against the RefSeq_mrna database using the script below. Everything seems to work smoothly if I use nt or other databases, however if I search against the RefSeq_mrna db (typing refseq_rna when prompted) my output file cannot be opened. Is there a specific designation for the RefSeq_mrna db in Bio::Tools::Run::RemoteBlast? The link http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html is no longer available.
> 
> Any suggestions would be appreciated,
> Mack
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