[Bioperl-l] reading gff3?

Smithies, Russell Russell.Smithies at agresearch.co.nz
Thu Mar 12 18:42:08 EDT 2009

What's the trick to reading the fasta attached to gff files?
Bio:FeatureIO and Bio::Tools::GFF both seem to ignore it (unless I'm doing it wrong)

What I'm trying to do is read in a gff3 file (with attached fasta) then get the sequence for the CDS features contained within.

Any ideas?



Russell Smithies 
Bioinformatics Applications Developer 
T +64 3 489 9085 
E  russell.smithies at agresearch.co.nz 
Invermay  Research Centre 
Puddle Alley, 
New Zealand 
T  +64 3 489 3809   
F  +64 3 489 9174  

Toitu te whenua, Toitu te tangata 
Sustain the land, Sustain the people 

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