[Bioperl-l] getting upstream regions

[Josh Burdick]

I was wondering what the current standard way to get sequence just
upstream of a gene was in bioperl.  We're mostly using the UCSC
dataset/tools at the moment.

At the moment, we're using a Perl module which calls the "nibFrag"
program from UCSC.  If people think this would be useful, I'd be
happy to contribute it, although I don't know bioperl's object
system terribly well, so it would probably need some rewriting.
(I gather there's some C code to do this, but the actual "nibFrag" 
program itself is quite fast, and this avoids making native calls,
which is nice, although slower.)

Josh
-- 
Josh Burdick
jburdick at gradient.cis.upenn.edu
http://www.cis.upenn.edu/~jburdick