[Bioperl-l] Re: mzef parser

Mon, 31 Jul 2000 18:57:09 +0100

Jason,

for some or another reason I am unable to reach you by email to
jason@chg.mc.duke.edu (the failure report just says '2'). So, maybe you can
get this through the list.

     Hilmar

Jason,

I'd be happy, too, to put something together with you. The only constraint
I'm currently facing is that I'm under heavy time pressure because I have
to get a local analysis pipeline up-and-running as quickly as possible, and
I have to invest the next two weeks in getting my poster ready for the
upcoming ISMB. So, right now I can't contribute much more than hacking
together something that at least offers the chance to be tidied up later.

And yes, please feel free to share your thoughts and design you have come
up with so far. I myself haven't designed yet something with respect to
gene structure prediction that could still hold in the big sense, but
mainly due to limited time. My initial idea was a feature container with
additional methods for safely and easily getting at promotor, exons,
introns, etc.

     Hilmar

Jason Stajich <jason@chg.mc.duke.edu>@chg.mc.duke.edu on 31.07.2000
15:02:58

Sent by:  jason@chg.mc.duke.edu

To:   HILMAR LAPP/PH/Novartis@PH
cc:   Bioperl <bioperl-l@bioperl.org>
Subject:  mzef parser

I need a MZEF parser/annotator as well as some other prediction software.

I have thinking about Analysis objects in the big sense.  A Bioperl object
that could generically add annotations parsed from various analysis
procedures would be the idea.  I am thinking about this model being used
for both Biocorba objects (to make distributing analysis easy) and the
ensembl-lite analysis pipeline.

So I'd be happy to work with you to design something and put it into play.

-Jason

Jason Stajich
jason@chg.mc.duke.edu
http://galton.mc.duke.edu/~jason/
(919)684-1806 (office)
(919)684-2275 (fax)
Center for Human Genetics - Duke University Medical Center
http://wwwchg.mc.duke.edu/