[Biojava-l] newbie question about gff

[Rusch, Michael]

Newbie question:

I want to read in a GFF file and process it taking full advantage of the gene model (e.g. exons belong to a transcript).  I see that I can read the GFF into an EntrySet, and then annotate a Sequence with the EntrySet, but I don't have a sequence to start off with.  I could read in sequence from a FASTA file, but since I'm not actually using sequence, and I'm dealing with human chromosomes, it seems quite wasteful to do so.  I could also just use the EntrySet, but then I can't take advantage of the gene model.  Is there a way to get a Sequence object with no sequence, just features from a GFF file?

Thanks,
Michael

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