[Bioperl-l] SeqFeature::Generic 'frame' method

[Hilmar Lapp]

Jason Stajich wrote:
> 
> That does seem safer.  I can easily transform from 1,2,3 to 0,1,2
> so frame +1 in blast will be equivalent to frame 0 in GFF. But what about
> cases where we don't have a frame, is Frame 0 technically correct there?

Is it possible to get frame 0 in a TBLASTN match? I don't really know
what this would mean. (for the risk of embarrassing myself, TBLASTN is
DNA/DNA on the protein level, right? So you have a frame for both
alignment partners, right?)

> 
> Strand information for a HSP currently comes from direction
> of start/end points on the query seq.  Is it concievable that they
> wouldn't match?  i.e. will a match in -3 frame always correspond to a
> match on rev strand of query....  This might be a dilhema...  I already

It's hard to conceive that they don't match always. Why would you
report a minus strand for a match that was translated from a forward
frame?

> checked in code which breaks because of invalid frames, I will fix so it
> is at least transformed to valid number space of gff.  Strand will get
> ignored for now.

We should fix this until the release. TBLASTN frame -3 is not the same
as +3 for someone who wants to extract the amino acid sequence that
led to the match.

	Hilmar
-- 
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Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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