[Bioperl-l] Don't want to donwload sequence contigs!

Jonathan Manning bmb9jrm at bmb.leeds.ac.uk
Thu Apr 22 09:43:11 EDT 2004

Hi all,

I'm new to bioperl, if this is the wrong place to post this sort of
question, someone let me know!

I'm working on a bioinformatics thesis project, and am using bioperl. At
the moment, I'm writing a script which constructs a
Bio::DB::Query::GenBank object with a query id or name, which is then
passed to a new Bio::DB::GenBank object. Trouble is, if Entrez comes up
with a contig, things freeze right out because the file's so big.

Question: is there a way to exclude contigs from a search, or else find
out the accession numbers which relate to a particular id, so that "NT_"
accessions can be excluded before a stream to GenBank is established? 

Appreciate any help,


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