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

[Dave Messina]

Aha, great, thanks for clarifying, Peter.

And if I bothered to look at the Bio::Tools::GFF documentation before answering :), I would have seen this:

    http://doc.bioperl.org/bioperl-live/Bio/Tools/GFF.html#General

which describes how you can use

    $gffio->get_seqs()


and related methods to pull out the sequence data.


Dave




On Aug 26, 2010, at 11:02, Peter wrote:

> 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