[Bioperl-l] Obtaining Refseq status with eutils

Michael Muratet mmuratet at hudsonalpha.org
Tue Nov 16 21:56:08 UTC 2010


I have been trying to get to the Refseq status info that shows up NCBI  
gene webpage. My latest attempt is:

my @accs = qw(SAAV_0049);

my $factory = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                        -email => 'mmuratet at hudsonalpha.org 
                                        -db    => 'gene',
                                        -term  => join(',', at accs));

my @uids = $factory->get_ids;

$factory->reset_parameters(-eutil => 'elink',
                            -dbfrom => 'gene',
                            -db => 'nuccore',
                            -linkname => 'gene_nuccore_refseqgene',
                            -id    => \@uids);

$factory->get_Response(-file => 'temp.txt');

All I get back is the ID number I gave it. Also, $factory->next_DocSum  
returns nothing.

A big part of the problem is that I don't know what field I'm looking  
for. I am also unsure that I am using the elink interface properly.

Does anyone know how to get to the Refseq data for a gene? I am  
looking for evidence of expression of gene models--is there a better  
annotation to use?



Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806

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