[Bioperl-l] Location mapping question

[Jason Stajich]

Try:
Bio::Coordinate::GeneMapper.

To see it in action: here is a script which maps protein domain/FASTP  
hits back to the Genome.
http://fungal.genome.duke.edu/~jes12/software/scripts/ 
map2genome.perl.txt

The downside is this can be a little slow.

-jason

On Nov 9, 2005, at 1:17 PM, Sean Davis wrote:

> I think I have seen code to do this kind of thing--hence this  
> email--but I
> may be mistaken.  I have oligo sequences mapped to mRNAs by blat  
> and have
> blat alignments to the genome.  Is there a way to quickly align the  
> oligos
> to the genome given this information using a bioperl module.  (Like  
> I said,
> I just can't seem to find it).
>
> Thanks,
> Sean
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12