[Bioperl-l] SwissProt and Subcellular localization information

Daniel Gaston daniel.gaston at gmail.com
Wed Nov 4 12:12:10 EST 2009


Sorry folks, it appears I was just being a bonehead and didn't look close
enough into Bio:Annotations and Bio:Species objects that store all of this
data.

Dan

On Wed, Nov 4, 2009 at 1:00 PM, <bioperl-l-request at lists.open-bio.org>wrote:

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>   1.  SwissProt and Subcellular localization information
>      (Daniel Gaston)
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>
> ---------- Forwarded message ----------
> From: Daniel Gaston <daniel.gaston at gmail.com>
> To: bioperl-l at lists.open-bio.org
> Date: Wed, 4 Nov 2009 10:45:04 -0400
> Subject: [Bioperl-l] SwissProt and Subcellular localization information
> Hi Everyone,
>
> I have recently been playing around with SwissProt format flatfiles and
> want
> to extract sequences based on subcellular localization. I notice in going
> through the code for swiss.pm and swissdriver.pm that in both (more so in
> swissdriver.pm) there are several steps where organelle information based
> on
> the OG line could be extracted and added to data structure but isn't. It
> seems that in both cases the OG line is being added in to the generic
> lumping of data from the OC, OS, and OX lines in order to extract species
> names and taxonomy information but getting rid of everything else. Is there
> a particular reason for this or just a simple oversight? On the surface at
> least it looks like a relatively simple modification to make although I
> admit that I am not terribly adept at manipulating these SeqIO
> datastructures.
>
> Thanks for your time,
>
> Dan
>
>
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