[Bioperl-l] Genbank query problem

Federico Abascal fedeabascal at yahoo.es
Sat Sep 29 06:47:09 EDT 2012

Dear colleagues,

I have a script (mitobank.pl) that is used by some people. It is aimed to retrieve mitochondrial genomes for a given taxonomic id. The problem arose when, some months ago, the NCBI reorganized the way genomes are queried and the script no longer worked. I have tried modifying the query string with no success.

What the script asked for was like:

my $seq;
my $gb = new Bio::DB::GenBank;
my $query = Bio::DB::Query::GenBank->new
(-query   =>(txid314147[Organism:exp] AND mitochondrial[title] AND genome[ti] NOT plasmid[title] NOT chromosome NOT chloroplast) OR (txid314147[Organism:exp] AND mitochondrion[title] AND genome[ti] NOT plasmid[title] NOT chromosome NOT chloroplast),
 -db      => 'genome');

It used to return the list of genomes available for that taxonomic id. However, the NCBI now returns a different kind of results.
I tried to modify the script and query the "nucleotide" database, but this does not work properly.

Any one could help me, please?

Thanks in advance,

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