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annotating to pseudogenes

Peter D'Eustachio eustachi at cshl.edu
Tue Mar 14 09:00:15 PST 2006


Two issues are lumped together here, I think.

The first is the amount and quality of data needed to justify a functional 
annotation, and clearly there are times when one annotation group wants to 
assert a conclusion that someone else finds questionable.

The second is the correct usage of the GO/SO noun, "pseudogene". Here, it 
seems very clear that this noun is only to be used when your own reasoning 
process, described as issue 1, has led you to the conclusion that the DNA 
sequence in question is really, most sincerely dead. If it's still 
twitching, or twitching in unexpected ways, according to the data in 
question as you interpret them, then it's not a GO pseudogene, by 
definition.

Peter D'Eustachio

----- Original Message ----- 
From: "Fiona McCarthy" <fmccarthy at cvm.msstate.edu>
To: <annotation at genome.stanford.edu>
Sent: Tuesday, March 14, 2006 11:35 AM
Subject: annotating to pseudogenes


> Hi All,
>
> I recent found a microarray tiling paper (PMID: 15876366) where the
> authors estimated that one fifth of human pseudogenes on chr22 are
> potentially transcribed. It seems to me that there must be a reason for
> this level of transcription, even if we don't know what it is.
>
> I think it would be reasonable to annotate pseudogenes to GO, even if we
> have to use function unknown in most cases. Otherwise, we would be
> implying that *all* pseudogenes have no function, and this may not be the
> case.
>
> As for the SO definition of a pseudogene, I am not sure that I would say
> that all pseudogenes are non-functional.
>
> Fiona
>
>
> AgBase Biocurator
> Department of Basic Sciences
> Box 6100
> MS 39762-6100
> Mississippi State University
> USA
> Tel:   (+ 1) 662 325 5859
> Fax:  (+ 1) 662 325 1031
>
> http://www.agbase.msstate.edu/
>
> 



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