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

Hilmar Lapp lapp@gnf.org
Mon, 26 Feb 2001 15:15:04 -0800

Jason Stajich wrote:
> Currently we only support frames of 0,1,2 as part of gff support I'm sure.
> However, as I try and map a TBLASTN HSP to a SeqFeature, frames
> can be -3,-2,-1,0,1,2,3.  Does anyone see problems with extending the
> supported values in the frame method to handle those above.  Does this
> break GFF standards somehow?  I can imagine someone parsing a blast
> report and writing the HSPs out as GFF features so it is quite likely that
> the two cases shall meet.

Hmm. As long as there's a clear context of an HSP being the result of
parsing a Blast report there's no problem with extending the set of
allowed values. However, as soon as this context gets lost, like you
said (and going through GFF is not the only way to lose that), there's
a problem, because then frame 1 and frame 1 no longer mean the same
thing. Bad.

Can we map TBLASTN frame to the definitions we have set forth in
SeqFeatureI? E.g. TBLASTN parsed frame -3 would become SeqFeatureI
strand -1, frame 2. TBLASTN parsed frame 1 would be mapped to strand
1, frame 0, and so forth. This would keep both the definitions and the
TBLASTN information.

The only remaining problem is TBLASTN frame 0. What does it mean? If
it's no frame, then it's equivalent to SeqFeatureI frame 0.

What do you think?

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