[Bioperl-l] EUtilities - pipeline - Exonic Structure

Anthony Ferrari ferraria at gmail.com
Wed May 16 14:38:47 UTC 2007

Hi all,

I want to do something relatively simple and I want to know how far Bioperl
tools could help me because I'm having troubles to get to the point.
Here is the pipeline :

"EntrezGene Query" ----- (esearch) -----> "Gene ID" ------ (*) ----->

(*) :
>From the EntrezGene ID, I want to retrieve the structure of the gene which
means having the whole genomic sequence and having the start and end
positions of each exons, introns, UTR'....

I thought of 2 ways to accomplish that :

  -  use 'efetch', get raw xml or asn1 and then parse it to obtain the
desired positions.
     this method should work but would take a little time to be ok.

  -  use Bio::DB::EntrezGene module with the "get_Seq_by_id" function. I
obtain a Bio::Seq object but I am not able to find any features stored in
it. So it doesn't seem that the get_Seq_by_id function get all information
contained in a EntrezGene entry (?) .

Can somebody help me to make the right choice or show me the right way?

I also saw that some packages detinated to deal with  gene structure exist
but I don't manage to know how to use it properly and even how to create one
of those objects !
Are those packages currently usable ?

Thanks in advance.
Best regards,

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