Bioperl: Feature mapping.. clone to contig and vice versa

[Ewan Birney]

On Mon, 27 Mar 2000, Jason Stajich wrote:

> I would be interested in this Doug and would be willing to lend some help.  
> I know this something my researchers need to be able to do better.


I wonder if you have walked around the ensembl code. It is built on top of
bioperl, is open source and coordinated from 

http://www.ensembl.org/

You should be able to cannabalise ensembl stuff to do some of what you
want. In addition, I feel ensembl is a good basis to do this sort of work. 
(doug - it is possible that you want this code to parse ensembl flat
files, in which case we can certainly give you better information than
EMBL flat files in ensembl). 


Ensembl is an open read-only cvs server. Also look at the ensembl mailing
list for more information on the current state of ensembl.


> 
> Jason
> On Fri, 24 Mar 2000, Doug Hyatt wrote:
> 
> > 
> > Hello,
> > 
> > I am looking for a script or routine that maps
> > feature coordinates (i.e. of genes, exons, repeats, etc.)
> > from their positions in a clone to the corresponding
> > positions in the contig and vice versa (from contig to
> > clone).   
> > 
> > Has such a routine been written for BioPerl?  If 
> > not, I will be writing one... is there interest in
> > this?
> > 
> > regards,
> > Doug Hyatt
> > Computational Biosciences
> > Oak Ridge National Laboratory
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> 
> Jason Stajich
> Center for Human Genetics
> Duke University Medical Center
> jason@chg.mc.duke.edu
> (919)684-1806
> http://www.duke.edu/~jes12/
> 
> 
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