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

[Judith Blake]

I agree too.  This is too far from ISS as now employed.

aren't these from older papers?  Isn't there better evidence available 
now?  if so, why include them?  if not, what about EXP?

judy

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
> > > > *****************************************************************
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