SwissProt and Subcellular localization information

[Daniel Gaston]

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
_______________________________________________
Bioperl-l mailing list
Bioperl-l@...
http://lists.open-bio.org/mailman/listinfo/bioperl-l

[Daniel Gaston]

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@...>wrote:

> Send Bioperl-l mailing list submissions to
>        bioperl-l@...
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://lists.open-bio.org/mailman/listinfo/bioperl-l
> or, via email, send a message with subject or body 'help' to
>        bioperl-l-request@...
>
> You can reach the person managing the list at
>        bioperl-l-owner@...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bioperl-l digest..."
>
> Today's Topics:
>
>   1.  SwissProt and Subcellular localization information
>      (Daniel Gaston)
>
>
> ---------- Forwarded message ----------
> From: Daniel Gaston <daniel.gaston@...>
> To: bioperl-l@...
> 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
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

_______________________________________________
Bioperl-l mailing list
Bioperl-l@...
http://lists.open-bio.org/mailman/listinfo/bioperl-l