[GMOD-devel] Re: [Open-bio-l] RE: seqfeature

[Lincoln Stein]

Thomas's suggestion is proper.  By the same token, score and strand
should also be optional qualifiers.  The Bio::DB::GFF schema, which
was based directly on GFF, has these mostly empty columns for phase,
score and strand which are wasteful and unattractive.

Lincoln

Thomas Down writes:
 > On Wed, May 01, 2002 at 10:58:42AM -0700, Hilmar Lapp wrote:
 > > I guess I should have said seqfeature (and there is a StrandedFeature or something in BioJava isn't there?). Also, I cared much more about the frame, which is absent too. Wouldn't you want to know the frame for a translation feature?
 > 
 > Yes, frame is kind-of useful occasionally, if you're dealing
 > with partial CDS.  It's also, of course, important if you're
 > writing an ensembl-style `gene builder'.  My point was that
 > for an everything other than coding exons (or DNA-protein 
 > alignment results, which amount to almost the same thing), it
 > seems to be a meaningless concept.  Perhaps I misunderstood
 > your original post, but it sounded as though you wanted frame
 > added as an extra column somewhere in the schema.  I just think
 > it should be an optional property (in the qualifier_value table)
 > for those types of feature where it's meaningful.
 > 
 > Does this make sense?
 > 
 >      Thomas.
 > 
 > 
 > PS.  BioJava also allows you to represent features with
 >      frames, when necesary (the FramedFeature interface).
 > 
 > 
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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
Positions available at my lab: see http://stein.cshl.org/#hire
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