[Bioperl-l] SwissProt and Subcellular localization information

Daniel Gaston daniel.gaston at gmail.com
Wed Nov 4 09:45:04 EST 2009


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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