[Bioperl-l] get mRNA details for a gene

Ahmet Kurdoglu tgenahmet at gmail.com
Wed Dec 27 16:38:43 EST 2006


Hi,

This is my first message to the list. I hope I get it right. Here is what
I'm trying to accomplish:

Get the mRNA details for a given gene (ex. DNASE2B) from its GenBank file.

Using the web-interface I can search with this query:
DNASE2B [sym] AND homo sapiens [ORGN] (returns only one result if you search
'gene' database)
and get the GenBank file by clicking on NC_000001.9 and I can see the
details for its two mRNAs. (I eventually need to get exon locations for both
of its transcripts)

However trying to do this in Perl has proved to be very difficult for me.
I've tried various methods, including get_Seq_by_id, get_Seq_by_gi, and
get_Stream_by_query. Before I explain in detail what I did I'd like to hear
your ideas on how to accomplish this.

Thank you.


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