[Bioperl-l] getting DNA sequence for exon features from GFF

[Peter]

On Thu, Aug 26, 2010 at 9:53 AM, Dave Messina <David.Messina at sbc.su.se> wrote:
>
> Admittedly i'm not up on the latest uses of GFF, but as far as I know, GFF
> is an annotation format only — it does not contain the actual sequence.
>
> Have you looked in your GFF file to see if there are nucleotides in there?
>
> Dave

Actually a GFF file can optionally include a FASTA format sequence
at the end of the file, although it seems to be more common to just
supply separate GFF and FASTA files and cross reference by ID.

Peter