[Bioperl-l] your bioperl module (fwd)

Hilmar Lapp hlapp@gmx.net
Tue, 30 Apr 2002 23:47:21 -0700 (PDT)

I'm forwarding this message to the list because of the much bigger
audience. -hilmar

---------- Forwarded message ----------
Date: Thu, 4 Apr 2002 11:56:55 -0500
From: J. David Rawn <jdrawn@towson.edu>
To: hlapp@gmx.net
Subject: your bioperl module

Hello Hilmar:

I am new to Bioperl (and only a beginning Perl programmer), and I would 
like to ask you a question about your transcript module.

I would like to create a database of an entire genome's transcripts, 
including upstream promoters,   (which of course are not transcribed), 
introns and exons and down stream elements up to 1000 nt beyond the 
polyA site. It looks to me as if your module performs exactly that 
function. My simple (minded) question is: how can one create such a 
database? I can naturally download entire chromosomes, entire sets of 
genes, etc, but the region surrounding each gene seems more problematic 
to me, and I cannot figure out how to do it. Is it just the case that 
your program runs and that's the solution?


David Rawn