[Bioperl-l] PROPOSED new method Bio::Range->offsetStranded

Sendu Bala bix at sendu.me.uk
Wed Jan 10 12:11:35 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 :)


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