[Bioperl-l] Bio::DB::GFF again

Aaron Mackey ajmackey at gmail.com
Tue Mar 3 11:06:08 EST 2009


The short answer is no, not directly.

But, take a look at Bio::Coordinate::GeneMapper; you can use this module (in
combination with features retrieved from a Bio::DB::GFF data source) to do
the necessary translation of coordinates from protein domain space into
genomic/CDS coordinates.

-Aaron

On Mon, Mar 2, 2009 at 10:49 PM, Alper Yilmaz <alperyilmaz at gmail.com> wrote:

> I have another question about Bio::DB::GFF module. I went through the
> manual
> couldn't find the answer. Maybe it's easy solution and I don't know it.
>
> Is it possible to overlay protein domain coordinates on genomic coordinates
> in Bio::DB::GFF?
> Let's say I want to extract -nucleotide sequence- of a protein domain. If
> my
> input is protein domain location (as amino acid coordinates) can I have dna
> sequence by using Bio::DB::GFF for the same region, (excluding intron
> sequences)?
>
> thanks,
>
> Alper Yilmaz
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