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

Peter biopython at maubp.freeserve.co.uk
Thu Aug 26 05:02:53 EDT 2010

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.


More information about the Bioperl-l mailing list