[Annotation] [Evidence] Fwd: ISS/ISA from Southerns?

[Valerie Wood]

I prefer IPI with the accession of the DNA molecule

Val

MICHELLE GIGLIO wrote:
>
>
> Hi Rama,
>
> I agree with Susan.  I am reluctant to add this back to ISS.  However, 
> I don't know where it would go instead.
>
> If it does come back to the ISS family (if we can not think of another 
> alternative) then it definitely can NOT go under ISA as there is no 
> alignment in this situation. It would have to be plain ISS.  (But I 
> still don't like it there.)
>
> Could it possibly be an IPI?
>
> Michelle
>
>
>
>
> -----Original Message-----
> From: evidence-bounces at genome.stanford.edu on behalf of Susan Tweedie
> Sent: Wed 6/4/2008 5:17 AM
> To: Rama Balakrishnan
> Cc: Evidence Code Group; GO Annotation list
> Subject: Re: [Evidence] Fwd:  ISS/ISA from Southerns?
>
> One thing we'd have to consider if we added this (back?) to ISS is that
> the new classification of evidence codes groups ISS, ISA etc as
> 'computational analysis evidence codes' - that wouldn't be strictly true
> if Southerns were included.
>
> I am uneasy about mixing together cases where the sequence is known with
> those that aren't - no review of the evidence is possible in the latter
> case. Personally, I would be reluctant to make an annotation based on a
> cross-hybridisation expt but maybe I just remember too many spurious
> bands from my time in the lab. 
>
> Are there really that many cases these days where sequencing is so
> stnadard where this is the only evidence to support a term? Maybe I'm
> just spolit working on a species with complete genome sequence...
>
> Cheers,
>
> Susan
>
>
>
>
>
> On Tue, 2008-06-03 at 12:05 -0700, Rama Balakrishnan wrote:
> > I haven't heard from anybody on this so far. Is it okay if we add
> > 'southern analysis' as an acceptable evidence to the ISS
> > documentation?
> >
> >
> > Thanks,
> >
> >
> > Rama
> >
> >
> > Begin forwarded message:
> >
> > > From: Rama Balakrishnan <rama at genome.stanford.edu>
> > > Date: May 9, 2008 5:18:06 PM PDT
> > > To: Evidence Code Group <evidence at genome.stanford.edu>
> > > Cc: GO Annotation list <annotation at genome.stanford.edu>
> > > Subject: [Evidence] ISS/ISA from Southerns?
> > >
> > >
> > > Reposting...
> > > I am dealing with a similar situation like the one Julie has
> > > mentioned below.
> > >
> > >
> > > Thanks,
> > >
> > >
> > > Rama
> > >
> > >
> > > Begin forwarded message:
> > > > From: Julie Park <juliep at genome.stanford.edu>
> > > > Date: April 23, 2008 3:57:22 PM PDT
> > > > To: evidence at genome.stanford.edu
> > > > Subject: [Evidence] ISS/ISA from Southerns?
> > > >
> > > >
> > > > Dear evidence code group,
> > > >
> > > > I had a question about whether Southern analysis alone can be used
> > > > as 
> > > > evidence for an annotation.
> > > >
> > > > In S. cerevisiae, MEL2-10 are annotated by ISS to
> > > > alpha-galactosidase 
> > > > activity.  There is no sequence alignment or information (older 
> > > > literature, pre-genome sequencing), instead the authors infer
> > > > homology/
> > > > sequence similarity from a Southern hybridization using a MEL1
> > > > probe.  
> > > > Southern analysis was listed in the old ISS documentation but the
> > > > only 
> > > > mention of Southerns in the new documentation is under ISA in 
> > > > conjunction with a sequence alignment.
> > > >
> > > > Is ISS by Southern only no longer allowed or did it just get left
> > > > out 
> > > > of the current documentation?
> > > > If allowed, would I leave these annotations as ISS or would it be
> > > > okay 
> > > > to ISA w/ MEL1?
> > > >
> > > > thanks,
> > > > Julie
> > > >
> > > > ****************************************************************
> > > > Julie Park, Ph.D., Scientific Curator
> > > >  Saccharomyces Genome Database
> > > >  Department of Genetics
> > > >  Stanford University School of Medicine
> > > >  Stanford, CA 94305-5120 USA
> > > >  phone: (650)724-9959  fax: (650)725-1534
> > > >  http://www.yeastgenome.org
> > > > *****************************************************************
> > > > _______________________________________________
> > > > Evidence mailing list
> > > > Evidence at geneontology.org
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> > >
> > >
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> >
> >
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Valerie Wood			 Tel: 01223 496909
S. pombe Genome Project		 Fax: 01223 494919 		       
Wellcome Trust Sanger Institute	 email: val at sanger.ac.uk
Wellcome Trust Genome Campus	 http://www.genedb.org/genedb/pombe 
Hinxton, Cambridge, CB10 1HH	 http://www.sanger.ac.uk/Projects/S_pombe



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