[Bioperl-l] PROPOSED new method Bio::Range->offsetStranded
cjfields at uiuc.edu
Wed Jan 10 12:17:40 EST 2007
> Cook, Malcolm wrote:
> > Hi Chris,
> > In part of a pipeline to design oligo microarray for detecting
> > alternate splice sites, I build 0-length features which
> identify the
> > location of all 5' and 3' splice sites (as inferred from
> flybase GFF
> > gene, transcript, mRNA, exon features) and then offset
> these feature
> > to create a region flanking it, which is then taken as the
> target of
> > an oligo design process.
> > I'm sure I could re-conceptualize my approach, but, as
> implemented, it
> > works a treat.
> > My thinking is influenced by my Excel's object model (VBA),
> which has
> > Offset as a destructive method of Excel.Range (of excel cells).
> > I suppose any algorithm that used a 'sliding window' could possibly
> > benefit from Bio::Range->offsetStranded.
> > Cheers,
> > Malcolm Cook (poised to commit ;)
> Sounds good to me. I didn't understand before why you'd have
> different start and end offsets, but now all is clear :)
Same here. Commit away I say!
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